von Hippel-Lindau disease tumor suppressor
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count | Chain A； UniProt 54–213 | Not recorded | Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） A1L66 ASP3082 × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；296 K；bis-tris propane, sodium formate, PEG3350 | Resolution 3.18 Å R-free 0.305 |
| 3 | Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count | Chain E； UniProt 54–213 | Not recorded | Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；296 K；bis-tris propane, sodium formate, PEG3350 | Resolution 3.18 Å R-free 0.305 |
| 5 | Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count | Chain I； UniProt 54–213 | Not recorded | Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；296 K；bis-tris propane, sodium formate, PEG3350 | Resolution 3.18 Å R-free 0.305 |
| 7 | Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count | Chain M； UniProt 54–213 | Not recorded | Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；296 K；bis-tris propane, sodium formate, PEG3350 | Resolution 3.18 Å R-free 0.305 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 9L6F | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1LM8 Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex Deposited 2002-04-30 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
54–213（160 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 1.85 Å R-free 0.236 |
| 1LQB Crystal structure of a hydroxylated HIF-1 alpha peptide bound to the pVHL/elongin-C/elongin-B complex Deposited 2002-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
52–213（162 aa）
Fragment：residues 52-213
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；HEPES, PEG2000 monomethylester, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.277 |
| 1LQB Crystal structure of a hydroxylated HIF-1 alpha peptide bound to the pVHL/elongin-C/elongin-B complex Deposited 2002-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
52–213（162 aa）
Fragment：residues 52-213
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；HEPES, PEG2000 monomethylester, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.277 |
| 1VCB THE VHL-ELONGINC-ELONGINB STRUCTURE Deposited 1999-03-13 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.7；10-15% PEG 2000, 200MM MAGNESIUM ACETATE, 100MM SODIUM CACODYLATE PH 5.7
|
Resolution 2.70 Å R-free 0.289 |
| 1VCB THE VHL-ELONGINC-ELONGINB STRUCTURE Deposited 1999-03-13 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.7；10-15% PEG 2000, 200MM MAGNESIUM ACETATE, 100MM SODIUM CACODYLATE PH 5.7
|
Resolution 2.70 Å R-free 0.289 |
| 1VCB THE VHL-ELONGINC-ELONGINB STRUCTURE Deposited 1999-03-13 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.7；10-15% PEG 2000, 200MM MAGNESIUM ACETATE, 100MM SODIUM CACODYLATE PH 5.7
|
Resolution 2.70 Å R-free 0.289 |
| 1VCB THE VHL-ELONGINC-ELONGINB STRUCTURE Deposited 1999-03-13 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.7；10-15% PEG 2000, 200MM MAGNESIUM ACETATE, 100MM SODIUM CACODYLATE PH 5.7
|
Resolution 2.70 Å R-free 0.289 |
| 3ZRC pVHL54-213-EloB-EloC complex (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE bound Deposited 2011-06-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | L8B (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1.M NA CITRATE PH 5.6, 0.2 M MG ACETATE, 15% PEG 8000, 50.MM DTT.
|
Resolution 2.90 Å R-free 0.350 |
| 3ZRC pVHL54-213-EloB-EloC complex (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE bound Deposited 2011-06-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | L8B (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1.M NA CITRATE PH 5.6, 0.2 M MG ACETATE, 15% PEG 8000, 50.MM DTT.
|
Resolution 2.90 Å R-free 0.350 |
| 3ZRC pVHL54-213-EloB-EloC complex (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE bound Deposited 2011-06-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | L8B (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1.M NA CITRATE PH 5.6, 0.2 M MG ACETATE, 15% PEG 8000, 50.MM DTT.
|
Resolution 2.90 Å R-free 0.350 |
| 3ZRC pVHL54-213-EloB-EloC complex (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE bound Deposited 2011-06-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | L8B (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1.M NA CITRATE PH 5.6, 0.2 M MG ACETATE, 15% PEG 8000, 50.MM DTT.
|
Resolution 2.90 Å R-free 0.350 |
| 3ZRF pVHL54-213-EloB-EloC complex_apo Deposited 2011-06-16 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CACODYLATE PH 5.8, 0.2 M MG ACETATE, 15% PEG8000, 5MM DTT.
|
Resolution 2.80 Å R-free 0.320 |
| 3ZRF pVHL54-213-EloB-EloC complex_apo Deposited 2011-06-16 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CACODYLATE PH 5.8, 0.2 M MG ACETATE, 15% PEG8000, 5MM DTT.
|
Resolution 2.80 Å R-free 0.320 |
| 3ZRF pVHL54-213-EloB-EloC complex_apo Deposited 2011-06-16 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CACODYLATE PH 5.8, 0.2 M MG ACETATE, 15% PEG8000, 5MM DTT.
|
Resolution 2.80 Å R-free 0.320 |
| 3ZRF pVHL54-213-EloB-EloC complex_apo Deposited 2011-06-16 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CACODYLATE PH 5.8, 0.2 M MG ACETATE, 15% PEG8000, 5MM DTT.
|
Resolution 2.80 Å R-free 0.320 |
| 3ZTC pVHL54-213-EloB-EloC complex _ (2S,4R)-N-((1,1'-biphenyl)-4-ylmethyl)- 4-hydroxy-1-(2-(3-methylisoxazol-5-yl)acetyl)pyrrolidine-2- carboxamide Deposited 2011-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | TR0 (4R)-N-(BIPHENYL-4-YLMETHYL)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50MM DTT.
|
Resolution 2.65 Å R-free 0.317 |
| 3ZTC pVHL54-213-EloB-EloC complex _ (2S,4R)-N-((1,1'-biphenyl)-4-ylmethyl)- 4-hydroxy-1-(2-(3-methylisoxazol-5-yl)acetyl)pyrrolidine-2- carboxamide Deposited 2011-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | TR0 (4R)-N-(BIPHENYL-4-YLMETHYL)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50MM DTT.
|
Resolution 2.65 Å R-free 0.317 |
| 3ZTC pVHL54-213-EloB-EloC complex _ (2S,4R)-N-((1,1'-biphenyl)-4-ylmethyl)- 4-hydroxy-1-(2-(3-methylisoxazol-5-yl)acetyl)pyrrolidine-2- carboxamide Deposited 2011-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | TR0 (4R)-N-(BIPHENYL-4-YLMETHYL)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50MM DTT.
|
Resolution 2.65 Å R-free 0.317 |
| 3ZTC pVHL54-213-EloB-EloC complex _ (2S,4R)-N-((1,1'-biphenyl)-4-ylmethyl)- 4-hydroxy-1-(2-(3-methylisoxazol-5-yl)acetyl)pyrrolidine-2- carboxamide Deposited 2011-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | TR0 (4R)-N-(BIPHENYL-4-YLMETHYL)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50MM DTT.
|
Resolution 2.65 Å R-free 0.317 |
| 3ZTD pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate Deposited 2011-07-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | ZTD METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50 MM DTT.
|
Resolution 2.79 Å R-free 0.309 |
| 3ZTD pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate Deposited 2011-07-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | ZTD METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50 MM DTT.
|
Resolution 2.79 Å R-free 0.309 |
| 3ZTD pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate Deposited 2011-07-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | ZTD METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50 MM DTT.
|
Resolution 2.79 Å R-free 0.309 |
| 3ZTD pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate Deposited 2011-07-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | ZTD METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50 MM DTT.
|
Resolution 2.79 Å R-free 0.309 |
| 3ZUN pVHL54-213-EloB-EloC complex_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol- 5-yl)acetyl)-N-(4-nitrobenzyl)pyrrolidine-2-carboxamide bound Deposited 2011-07-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：PVHL54-213, RESIDUES 54-213
|
Not recorded | GOL GLYCEROL × 1 ZUN (4R)-4-hydroxy-1-[(3-methyl-1,2-oxazol-5-yl)acetyl]-N-[(4-nitrophenyl)methyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.8, 0.2 M MG ACETATE, 15% PEG 8000, 50 MM DTT.
|
Resolution 2.50 Å R-free 0.302 |
| 3ZUN pVHL54-213-EloB-EloC complex_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol- 5-yl)acetyl)-N-(4-nitrobenzyl)pyrrolidine-2-carboxamide bound Deposited 2011-07-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：PVHL54-213, RESIDUES 54-213
|
Not recorded | ZUN (4R)-4-hydroxy-1-[(3-methyl-1,2-oxazol-5-yl)acetyl]-N-[(4-nitrophenyl)methyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.8, 0.2 M MG ACETATE, 15% PEG 8000, 50 MM DTT.
|
Resolution 2.50 Å R-free 0.302 |
| 3ZUN pVHL54-213-EloB-EloC complex_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol- 5-yl)acetyl)-N-(4-nitrobenzyl)pyrrolidine-2-carboxamide bound Deposited 2011-07-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：PVHL54-213, RESIDUES 54-213
|
Not recorded | ZUN (4R)-4-hydroxy-1-[(3-methyl-1,2-oxazol-5-yl)acetyl]-N-[(4-nitrophenyl)methyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.8, 0.2 M MG ACETATE, 15% PEG 8000, 50 MM DTT.
|
Resolution 2.50 Å R-free 0.302 |
| 3ZUN pVHL54-213-EloB-EloC complex_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol- 5-yl)acetyl)-N-(4-nitrobenzyl)pyrrolidine-2-carboxamide bound Deposited 2011-07-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：PVHL54-213, RESIDUES 54-213
|
Not recorded | ZUN (4R)-4-hydroxy-1-[(3-methyl-1,2-oxazol-5-yl)acetyl]-N-[(4-nitrophenyl)methyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.8, 0.2 M MG ACETATE, 15% PEG 8000, 50 MM DTT.
|
Resolution 2.50 Å R-free 0.302 |
| 4AJY von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide Deposited 2012-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
214–373（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M K PHOSPHATE PH 6.6 0.2 M (NH4)2SO4 20% PEG MME 5000 5 MM DTT
|
Resolution 1.73 Å R-free 0.232 |
| 4AWJ pVHL:EloB:EloC complex, in complex with capped Hydroxyproline Deposited 2012-06-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 3 V6F (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1 M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT
|
Resolution 2.50 Å R-free 0.264 |
| 4AWJ pVHL:EloB:EloC complex, in complex with capped Hydroxyproline Deposited 2012-06-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 1 V6F (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide × 1 ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1 M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT
|
Resolution 2.50 Å R-free 0.264 |
| 4AWJ pVHL:EloB:EloC complex, in complex with capped Hydroxyproline Deposited 2012-06-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 1 V6F (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1 M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT
|
Resolution 2.50 Å R-free 0.264 |
| 4AWJ pVHL:EloB:EloC complex, in complex with capped Hydroxyproline Deposited 2012-06-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 1 V6F (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1 M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT
|
Resolution 2.50 Å R-free 0.264 |
| 4B95 pVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide bound Deposited 2012-08-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | ACT ACETATE ION × 1 UCK (2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15 % PEG8000, 50MM DTT
|
Resolution 2.80 Å R-free 0.236 |
| 4B95 pVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide bound Deposited 2012-08-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | UCK (2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15 % PEG8000, 50MM DTT
|
Resolution 2.80 Å R-free 0.236 |
| 4B95 pVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide bound Deposited 2012-08-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | UCK (2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15 % PEG8000, 50MM DTT
|
Resolution 2.80 Å R-free 0.236 |
| 4B95 pVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide bound Deposited 2012-08-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Not recorded | UCK (2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15 % PEG8000, 50MM DTT
|
Resolution 2.80 Å R-free 0.236 |
| 4B9K pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide bound Deposited 2012-09-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | TG0 (2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CACODYLATE, PH 6.0, 0.2 M MG ACTETATE, 15% PEG3350, 5MM DTT
|
Resolution 2.00 Å R-free 0.220 |
| 4B9K pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide bound Deposited 2012-09-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | TG0 (2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide × 1 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CACODYLATE, PH 6.0, 0.2 M MG ACTETATE, 15% PEG3350, 5MM DTT
|
Resolution 2.00 Å R-free 0.220 |
| 4B9K pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide bound Deposited 2012-09-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | TG0 (2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide × 1 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CACODYLATE, PH 6.0, 0.2 M MG ACTETATE, 15% PEG3350, 5MM DTT
|
Resolution 2.00 Å R-free 0.220 |
| 4B9K pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide bound Deposited 2012-09-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | TG0 (2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide × 1 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M NA CACODYLATE, PH 6.0, 0.2 M MG ACTETATE, 15% PEG3350, 5MM DTT
|
Resolution 2.00 Å R-free 0.220 |
| 4BKS von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Deposited 2013-04-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 214-373
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | X6C (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1M NA CACODYALATE PH 6.0, 0.2M MG ACETATE, 15%PEG3350, 5MM DTT
|
Resolution 2.20 Å R-free 0.225 |
| 4BKS von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Deposited 2013-04-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 214-373
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | X6C (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1M NA CACODYALATE PH 6.0, 0.2M MG ACETATE, 15%PEG3350, 5MM DTT
|
Resolution 2.20 Å R-free 0.225 |
| 4BKS von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Deposited 2013-04-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 214-373
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | X6C (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1M NA CACODYALATE PH 6.0, 0.2M MG ACETATE, 15%PEG3350, 5MM DTT
|
Resolution 2.20 Å R-free 0.225 |
| 4BKS von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide Deposited 2013-04-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 214-373
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | X6C (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1M NA CACODYALATE PH 6.0, 0.2M MG ACETATE, 15%PEG3350, 5MM DTT
|
Resolution 2.20 Å R-free 0.225 |
| 4BKT von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide Deposited 2013-04-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QD0 (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT
|
Resolution 2.35 Å R-free 0.228 |
| 4BKT von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide Deposited 2013-04-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QD0 (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ARG ARGININE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT
|
Resolution 2.35 Å R-free 0.228 |
| 4BKT von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide Deposited 2013-04-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QD0 (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT
|
Resolution 2.35 Å R-free 0.228 |
| 4BKT von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide Deposited 2013-04-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Fragment：RESIDUES 54-213
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QD0 (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT
|
Resolution 2.35 Å R-free 0.228 |
| 4W9C pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(oxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 2) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JG (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-oxazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.251 |
| 4W9C pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(oxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 2) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JG (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-oxazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.251 |
| 4W9C pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(oxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 2) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JG (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-oxazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.251 |
| 4W9C pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(oxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 2) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JG (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-oxazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.251 |
| 4W9D pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methyloxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JK (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-oxazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.236 |
| 4W9D pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methyloxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JK (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-oxazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.236 |
| 4W9D pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methyloxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JK (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-oxazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.236 |
| 4W9D pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methyloxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JK (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-oxazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.236 |
| 4W9E pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 4) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JT (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.60 Å R-free 0.261 |
| 4W9E pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 4) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JT (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.60 Å R-free 0.261 |
| 4W9E pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 4) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JT (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.60 Å R-free 0.261 |
| 4W9E pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 4) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JT (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.60 Å R-free 0.261 |
| 4W9F pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 5) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JU (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.229 |
| 4W9F pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 5) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JU (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.229 |
| 4W9F pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 5) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JU (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.229 |
| 4W9F pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 5) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JU (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.229 |
| 4W9G pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(3-methyl-4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JV (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[3-methyl-4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.264 |
| 4W9G pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(3-methyl-4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JV (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[3-methyl-4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.264 |
| 4W9G pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(3-methyl-4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JV (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[3-methyl-4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.264 |
| 4W9G pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(3-methyl-4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JV (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[3-methyl-4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.264 |
| 4W9H pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 7) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JF N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.253 |
| 4W9H pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 7) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JF N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.253 |
| 4W9H pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 7) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JF N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.253 |
| 4W9H pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 7) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JF N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.253 |
| 4W9I pVHL:EloB:EloC in complex with (2S,4R)-1-((2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-carbonyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JS (4R)-1-acetyl-4-hydroxy-L-prolyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.40 Å R-free 0.275 |
| 4W9I pVHL:EloB:EloC in complex with (2S,4R)-1-((2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-carbonyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JS (4R)-1-acetyl-4-hydroxy-L-prolyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.40 Å R-free 0.275 |
| 4W9I pVHL:EloB:EloC in complex with (2S,4R)-1-((2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-carbonyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JS (4R)-1-acetyl-4-hydroxy-L-prolyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.40 Å R-free 0.275 |
| 4W9I pVHL:EloB:EloC in complex with (2S,4R)-1-((2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-carbonyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JS (4R)-1-acetyl-4-hydroxy-L-prolyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.40 Å R-free 0.275 |
| 4W9J pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-4-methylpentanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 13) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JH N-acetyl-L-leucyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.265 |
| 4W9J pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-4-methylpentanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 13) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JH N-acetyl-L-leucyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.265 |
| 4W9J pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-4-methylpentanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 13) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JH N-acetyl-L-leucyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.265 |
| 4W9J pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-4-methylpentanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 13) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JH N-acetyl-L-leucyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.265 |
| 4W9K pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 14) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JO N-acetyl-L-phenylalanyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.260 |
| 4W9K pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 14) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JO N-acetyl-L-phenylalanyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.260 |
| 4W9K pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 14) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JO N-acetyl-L-phenylalanyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.260 |
| 4W9K pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 14) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JO N-acetyl-L-phenylalanyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.260 |
| 4W9L pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3,3-dimethylbutanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 15) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JJ N-acetyl-3-methyl-L-valyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.243 |
| 4W9L pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3,3-dimethylbutanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 15) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JJ N-acetyl-3-methyl-L-valyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.243 |
| 4W9L pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3,3-dimethylbutanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 15) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JJ N-acetyl-3-methyl-L-valyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.243 |
| 4W9L pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3,3-dimethylbutanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 15) Deposited 2014-08-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 3JJ N-acetyl-3-methyl-L-valyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.243 |
| 4WQO Structure of VHL-EloB-EloC-Cul2 Deposited 2014-10-22 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–213（213 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；4M Na formate
|
Resolution 3.20 Å R-free 0.249 |
| 5LLI pVHL:EloB:EloC in complex with VH298 Deposited 2016-07-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 6Z3 (2~{S},4~{R})-1-[(2~{S})-2-[(1-cyanocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.40 Å R-free 0.252 |
| 5LLI pVHL:EloB:EloC in complex with VH298 Deposited 2016-07-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 6Z3 (2~{S},4~{R})-1-[(2~{S})-2-[(1-cyanocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.40 Å R-free 0.252 |
| 5LLI pVHL:EloB:EloC in complex with VH298 Deposited 2016-07-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 6Z3 (2~{S},4~{R})-1-[(2~{S})-2-[(1-cyanocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.40 Å R-free 0.252 |
| 5LLI pVHL:EloB:EloC in complex with VH298 Deposited 2016-07-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 6Z3 (2~{S},4~{R})-1-[(2~{S})-2-[(1-cyanocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.40 Å R-free 0.252 |
| 5N4W Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex Deposited 2017-02-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain V
54–213（160 aa）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris pH 7.6, 0.15 M ammonium sulphate, 15% polyethyleneglycol 4000 and 3% 1,4-dioxane or 4% acetonitrile. The sample was crystallised in the presence of a 19-mer peptide mimicking the substrate HIF-1alpha - residues 559-577 (DEALAPYIPMDDDFQLRSF, with the mutations L559D and M561A and P564 is hydroxyproline).
|
Resolution 3.90 Å R-free 0.346 |
| 5NVV pVHL:EloB:EloC in complex with (2S,4R)-4-hydroxy-1-((S)-2-(2-hydroxyacetamido)-3,3-dimethylbutanoyl)-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BT (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(2-oxidanylethanoylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.245 |
| 5NVV pVHL:EloB:EloC in complex with (2S,4R)-4-hydroxy-1-((S)-2-(2-hydroxyacetamido)-3,3-dimethylbutanoyl)-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BT (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(2-oxidanylethanoylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.245 |
| 5NVV pVHL:EloB:EloC in complex with (2S,4R)-4-hydroxy-1-((S)-2-(2-hydroxyacetamido)-3,3-dimethylbutanoyl)-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BT (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(2-oxidanylethanoylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.245 |
| 5NVV pVHL:EloB:EloC in complex with (2S,4R)-4-hydroxy-1-((S)-2-(2-hydroxyacetamido)-3,3-dimethylbutanoyl)-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BT (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(2-oxidanylethanoylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.245 |
| 5NVW pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BW (2~{S},4~{R})-1-[(2~{S})-2-(cyclopropylcarbonylamino)-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.249 |
| 5NVW pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BW (2~{S},4~{R})-1-[(2~{S})-2-(cyclopropylcarbonylamino)-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.249 |
| 5NVW pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BW (2~{S},4~{R})-1-[(2~{S})-2-(cyclopropylcarbonylamino)-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.249 |
| 5NVW pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BW (2~{S},4~{R})-1-[(2~{S})-2-(cyclopropylcarbonylamino)-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.249 |
| 5NVX pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-fluorocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 4YY N-[(1-fluorocyclopropyl)carbonyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.245 |
| 5NVX pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-fluorocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 4YY N-[(1-fluorocyclopropyl)carbonyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.245 |
| 5NVX pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-fluorocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 4YY N-[(1-fluorocyclopropyl)carbonyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.245 |
| 5NVX pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-fluorocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 4YY N-[(1-fluorocyclopropyl)carbonyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.245 |
| 5NVY pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamidopropanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl) pyrrolidine-2-carboxamide (ligand 11) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9B5 (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.90 Å R-free 0.269 |
| 5NVY pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamidopropanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl) pyrrolidine-2-carboxamide (ligand 11) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9B5 (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.90 Å R-free 0.269 |
| 5NVY pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamidopropanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl) pyrrolidine-2-carboxamide (ligand 11) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9B5 (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.90 Å R-free 0.269 |
| 5NVY pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamidopropanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl) pyrrolidine-2-carboxamide (ligand 11) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9B5 (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.90 Å R-free 0.269 |
| 5NVZ pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetylcyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 16) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BN (2~{S},4~{R})-1-[(2~{S})-2-[(1-ethanoylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.270 |
| 5NVZ pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetylcyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 16) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BN (2~{S},4~{R})-1-[(2~{S})-2-[(1-ethanoylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.270 |
| 5NVZ pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetylcyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 16) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BN (2~{S},4~{R})-1-[(2~{S})-2-[(1-ethanoylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.270 |
| 5NVZ pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetylcyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 16) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BN (2~{S},4~{R})-1-[(2~{S})-2-[(1-ethanoylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.270 |
| 5NW0 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetamidocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 17) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BK (2~{S},4~{R})-1-[(2~{S})-2-[(1-acetamidocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.30 Å R-free 0.238 |
| 5NW0 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetamidocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 17) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BK (2~{S},4~{R})-1-[(2~{S})-2-[(1-acetamidocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.30 Å R-free 0.238 |
| 5NW0 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetamidocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 17) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BK (2~{S},4~{R})-1-[(2~{S})-2-[(1-acetamidocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.30 Å R-free 0.238 |
| 5NW0 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetamidocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 17) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BK (2~{S},4~{R})-1-[(2~{S})-2-[(1-acetamidocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.30 Å R-free 0.238 |
| 5NW1 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclobutanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 18) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BH (2~{S},4~{R})-1-[(2~{S})-2-(cyclobutylcarbonylamino)-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.238 |
| 5NW1 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclobutanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 18) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BH (2~{S},4~{R})-1-[(2~{S})-2-(cyclobutylcarbonylamino)-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.238 |
| 5NW1 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclobutanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 18) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BH (2~{S},4~{R})-1-[(2~{S})-2-(cyclobutylcarbonylamino)-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.238 |
| 5NW1 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclobutanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 18) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9BH (2~{S},4~{R})-1-[(2~{S})-2-(cyclobutylcarbonylamino)-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.10 Å R-free 0.238 |
| 5NW2 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-3,3-dimethyl-2-(oxetane-3-carboxamido)butanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 19) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9B8 (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(oxetan-3-ylcarbonylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.242 |
| 5NW2 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-3,3-dimethyl-2-(oxetane-3-carboxamido)butanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 19) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9B8 (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(oxetan-3-ylcarbonylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.242 |
| 5NW2 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-3,3-dimethyl-2-(oxetane-3-carboxamido)butanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 19) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9B8 (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(oxetan-3-ylcarbonylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.242 |
| 5NW2 pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-3,3-dimethyl-2-(oxetane-3-carboxamido)butanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 19) Deposited 2017-05-04 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 9B8 (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(oxetan-3-ylcarbonylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.20 Å R-free 0.242 |
| 5T35 The PROTAC MZ1 in complex with the second bromodomain of Brd4 and pVHL:ElonginC:ElonginB Deposited 2016-08-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
54–213（160 aa）
|
Not recorded | 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；PEG 8000, Sodium citrate
|
Resolution 2.70 Å R-free 0.231 |
| 5T35 The PROTAC MZ1 in complex with the second bromodomain of Brd4 and pVHL:ElonginC:ElonginB Deposited 2016-08-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
54–213（160 aa）
|
Not recorded | 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；PEG 8000, Sodium citrate
|
Resolution 2.70 Å R-free 0.231 |
| 6BVB Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C Deposited 2017-12-12 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
1–160（160 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；26% (v/v) PEG-3350, 0.2 M Li2SO4, 0.1 M Bis-Tris. 7 mg/mL protein complex.
|
Resolution 2.00 Å R-free 0.235 |
| 6FMI pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-oxopropan-2-yl)acetamide (ligand 2) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV2 ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.80 Å R-free 0.256 |
| 6FMI pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-oxopropan-2-yl)acetamide (ligand 2) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV2 ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.80 Å R-free 0.256 |
| 6FMJ pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-Acetamidopropanethioyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl) benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV5 (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanethioyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.45 Å R-free 0.265 |
| 6FMJ pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-Acetamidopropanethioyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl) benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV5 (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanethioyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.45 Å R-free 0.265 |
| 6FMJ pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-Acetamidopropanethioyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl) benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV5 (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanethioyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.45 Å R-free 0.265 |
| 6FMJ pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-Acetamidopropanethioyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl) benzyl)pyrrolidine-2-carboxamide (ligand 3) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV5 (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanethioyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.45 Å R-free 0.265 |
| 6FMK pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-thioxopropan-2-yl)acetamide (ligand 4) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV8 ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-sulfanylidene-propan-2-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.75 Å R-free 0.260 |
| 6FMK pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-thioxopropan-2-yl)acetamide (ligand 4) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV8 ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-sulfanylidene-propan-2-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.75 Å R-free 0.260 |
| 6FMK pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-thioxopropan-2-yl)acetamide (ligand 4) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV8 ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-sulfanylidene-propan-2-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.75 Å R-free 0.260 |
| 6FMK pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-thioxopropan-2-yl)acetamide (ligand 4) Deposited 2018-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–204（151 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DV8 ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-sulfanylidene-propan-2-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.75 Å R-free 0.260 |
| 6GFX pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 13a) Deposited 2018-05-02 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；20-22% PEG MME 5000, 0.2 M ammonium sulfate, 0.1 M potassium phosphate, 10 mM DTT
|
Resolution 1.83 Å R-free 0.212 |
| 6GFY pVHL:EloB:EloC in complex with modified VH032 containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 14a) Deposited 2018-05-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EXH (2~{R},3~{R},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.258 |
| 6GFY pVHL:EloB:EloC in complex with modified VH032 containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 14a) Deposited 2018-05-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EXH (2~{R},3~{R},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.258 |
| 6GFY pVHL:EloB:EloC in complex with modified VH032 containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 14a) Deposited 2018-05-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EXH (2~{R},3~{R},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.258 |
| 6GFY pVHL:EloB:EloC in complex with modified VH032 containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 14a) Deposited 2018-05-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EXH (2~{R},3~{R},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.70 Å R-free 0.258 |
| 6GFZ pVHL:EloB:EloC in complex with modified VH032 containing (3S,4S)-3-fluoro-4-hydroxyproline (ligand 14b) Deposited 2018-05-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EXE (2~{R},3~{S},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.30 Å R-free 0.245 |
| 6GFZ pVHL:EloB:EloC in complex with modified VH032 containing (3S,4S)-3-fluoro-4-hydroxyproline (ligand 14b) Deposited 2018-05-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EXE (2~{R},3~{S},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.30 Å R-free 0.245 |
| 6GFZ pVHL:EloB:EloC in complex with modified VH032 containing (3S,4S)-3-fluoro-4-hydroxyproline (ligand 14b) Deposited 2018-05-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EXE (2~{R},3~{S},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.30 Å R-free 0.245 |
| 6GFZ pVHL:EloB:EloC in complex with modified VH032 containing (3S,4S)-3-fluoro-4-hydroxyproline (ligand 14b) Deposited 2018-05-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EXE (2~{R},3~{S},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；PEG 3350, MgOAc, Sodium cacodylate, DTT
|
Resolution 2.30 Å R-free 0.245 |
| 6GMN pVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-carboxylate Deposited 2018-05-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 2 F4E methyl 4~{H}-furo[3,2-b]pyrrole-5-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 1.94 Å R-free 0.244 |
| 6GMN pVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-carboxylate Deposited 2018-05-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 1.94 Å R-free 0.244 |
| 6GMN pVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-carboxylate Deposited 2018-05-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Not recorded | ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 1.94 Å R-free 0.244 |
| 6GMN pVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-carboxylate Deposited 2018-05-27 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 1 F4E methyl 4~{H}-furo[3,2-b]pyrrole-5-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 1.94 Å R-free 0.244 |
| 6GMQ pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol Deposited 2018-05-28 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 2.75 Å R-free 0.279 |
| 6GMQ pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol Deposited 2018-05-28 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 2.75 Å R-free 0.279 |
| 6GMQ pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol Deposited 2018-05-28 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 1 F4K (4-pyrrol-1-ylphenyl)methanol × 1 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 2.75 Å R-free 0.279 |
| 6GMQ pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol Deposited 2018-05-28 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ACT ACETATE ION × 1 F4K (4-pyrrol-1-ylphenyl)methanol × 1 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 2.75 Å R-free 0.279 |
| 6GMR pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol Deposited 2018-05-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
1–160（160 aa）
|
Not recorded | SO4 SULFATE ION × 1 F4K (4-pyrrol-1-ylphenyl)methanol × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M K phosphate pH 6.6, 0.2 M AS, 20% PEG MME 5000, 5% DTT
|
Resolution 1.75 Å R-free 0.235 |
| 6GMX pVHL:EloB:EloC in complex with 6-chlorothiochroman-4-one Deposited 2018-05-28 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | F7B 6-chloranyl-2,3-dihydrothiochromen-4-one × 1 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 2.53 Å R-free 0.361 |
| 6GMX pVHL:EloB:EloC in complex with 6-chlorothiochroman-4-one Deposited 2018-05-28 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | IPA ISOPROPYL ALCOHOL × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 2.53 Å R-free 0.361 |
| 6GMX pVHL:EloB:EloC in complex with 6-chlorothiochroman-4-one Deposited 2018-05-28 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 2.53 Å R-free 0.361 |
| 6GMX pVHL:EloB:EloC in complex with 6-chlorothiochroman-4-one Deposited 2018-05-28 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | F7B 6-chloranyl-2,3-dihydrothiochromen-4-one × 1 IPA ISOPROPYL ALCOHOL × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT
|
Resolution 2.53 Å R-free 0.361 |
| 6HAX Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2018-08-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–213（160 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 8 FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.75；277 K；13% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 8.0
|
Resolution 2.35 Å R-free 0.268 |
| 6HAX Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2018-08-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.75；277 K；13% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 8.0
|
Resolution 2.35 Å R-free 0.268 |
| 6HAY Crystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2018-08-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–213（160 aa）
|
Not recorded | FX8 (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 11 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.75；277 K；18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 7.75
|
Resolution 2.24 Å R-free 0.223 |
| 6HAY Crystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2018-08-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | FX8 (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 11 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.75；277 K；18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 7.75
|
Resolution 2.24 Å R-free 0.223 |
| 6HR2 Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB Deposited 2018-09-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
8–156（149 aa）
|
Not recorded | FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% (w/v) PEG1500, 0.1 M MIB Buffer, pH 6.0
|
Resolution 1.76 Å R-free 0.236 |
| 6HR2 Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB Deposited 2018-09-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
8–156（149 aa）
|
Not recorded | FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% (w/v) PEG1500, 0.1 M MIB Buffer, pH 6.0
|
Resolution 1.76 Å R-free 0.236 |
| 6I7Q Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form Deposited 2018-11-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
1–160（160 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；0.1M Cacodyl-Na pH 5.8, 0.1M Mg formate, 50 mM Cystamine, 22 % PEG3350
|
Resolution 1.80 Å R-free 0.237 |
| 6I7R Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form Deposited 2018-11-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
1–160（160 aa）
|
Not recorded | FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.8；293 K；0.1M Cacodyl-Na pH 5.8, 0.1M Mg Formate, 50mM Cystamine, 22% PEG3350
|
Resolution 1.95 Å R-free 0.203 |
| 6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain V
7–154（148 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；15 mM Hepes pH 7.5
100 mM NaCl
0.5 mM DTT
1% glycerol
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 8.40 Å |
| 6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric |
Chain V
1–160（160 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；15 mM HEPES pH 7.5
100 mM NaCL
0.5 mM DTT
1% Glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.20 Å |
| 6SIS Crystal structure of macrocyclic PROTAC 1 in complex with the second bromodomain of human Brd4 and pVHL:ElonginC:ElonginB Deposited 2019-08-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
54–213（160 aa）
|
Not recorded | LFE ~{N}-[(5~{S},7~{R},11~{S},23~{S})-11-~{tert}-butyl-34-(4-methyl-1,3-thiazol-5-yl)-7-oxidanyl-4,10,13-tris(oxidanylidene)-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.0^{5,9}]hexatriaconta-1(32),33,35-trien-23-yl]-2-[(7~{S},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10% (w/v) PEG 8000, 0.1 M Tris-HCl (pH 7.5) and 0.1 M MgCl2
|
Resolution 3.50 Å R-free 0.247 |
| 6SIS Crystal structure of macrocyclic PROTAC 1 in complex with the second bromodomain of human Brd4 and pVHL:ElonginC:ElonginB Deposited 2019-08-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
54–213（160 aa）
|
Not recorded | LFE ~{N}-[(5~{S},7~{R},11~{S},23~{S})-11-~{tert}-butyl-34-(4-methyl-1,3-thiazol-5-yl)-7-oxidanyl-4,10,13-tris(oxidanylidene)-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.0^{5,9}]hexatriaconta-1(32),33,35-trien-23-yl]-2-[(7~{S},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10% (w/v) PEG 8000, 0.1 M Tris-HCl (pH 7.5) and 0.1 M MgCl2
|
Resolution 3.50 Å R-free 0.247 |
| 6ZHC PROTAC6 mediated complex of VHL:EloB:EloC and Bcl-xL Deposited 2020-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain AAA
59–213（155 aa）
|
Not recorded | QL8 2-[8-(1,3-benzothiazol-2-ylcarbamoyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]-5-[3-[4-[3-[2-[2-[2-[2-[2-[3-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]prop-1-ynyl]phenoxy]propyl]-1,3-thiazole-4-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 17 GOL GLYCEROL × 9 IOD IODIDE ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；291 K；0.2 M Potassium iodide, 0.1 M MES pH 6.5, 23% PEG 4000
|
Resolution 1.92 Å R-free 0.196 |
| 7CJB VHL recognizes hydroxyproline in RIPK1 Deposited 2020-07-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
55–213（159 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.5；289 K；sodium cacodylate pH 6.5, 100 mM magnesium acetate, 15%(w/v) PEG 6000
|
Resolution 2.80 Å R-free 0.259 |
| 7CJB VHL recognizes hydroxyproline in RIPK1 Deposited 2020-07-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
55–213（159 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.5；289 K；sodium cacodylate pH 6.5, 100 mM magnesium acetate, 15%(w/v) PEG 6000
|
Resolution 2.80 Å R-free 0.259 |
| 7CJB VHL recognizes hydroxyproline in RIPK1 Deposited 2020-07-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
55–213（159 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.5；289 K；sodium cacodylate pH 6.5, 100 mM magnesium acetate, 15%(w/v) PEG 6000
|
Resolution 2.80 Å R-free 0.259 |
| 7CJB VHL recognizes hydroxyproline in RIPK1 Deposited 2020-07-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain M
55–213（159 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.5；289 K；sodium cacodylate pH 6.5, 100 mM magnesium acetate, 15%(w/v) PEG 6000
|
Resolution 2.80 Å R-free 0.259 |
| 7JTO Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB Deposited 2020-08-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
1–160（160 aa）
|
Not recorded | SCN THIOCYANATE ION × 4 EDO 1,2-ETHANEDIOL × 5 VKA 3-methyl-N-(11-{[2-(4-{[4'-(4-methylpiperazin-1-yl)-3'-{[6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carbonyl]amino}[1,1'-biphenyl]-3-yl]methyl}piperazin-1-yl)ethyl]amino}-11-oxoundecanoyl)-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium, pH 7.5-8.0, 1.3-1.6 M sodium thiocyanate, 15-20% PEG3350
|
Resolution 1.70 Å R-free 0.225 |
| 7JTP Crystal structure of Protac MS67 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB Deposited 2020-08-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
1–160（160 aa）
|
Not recorded | GOL GLYCEROL × 1 X6M N-(6-fluoro-3'-{[6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carbonyl]amino}-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-carbonyl)glycyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1 M Tris, pH 8.5, 30% PEG300
|
Resolution 2.12 Å R-free 0.224 |
| 7KHH Ternary complex of VHL/BRD4-BD1/Compound9 (4-(3,5-difluoropyridin-2-yl)-N-(11-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)amino)-11-oxoundecyl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[cd,f]azulene-6-carboxamide) Deposited 2020-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
55–213（159 aa）
|
Not recorded | WEP N-[11-({7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulene-9-carbonyl}amino)undecanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8；291 K；18% w/v PEG 8K, 10% v/v PEG 200, 0.1 M BIS-TRIS propane pH 9.0
|
Resolution 2.28 Å R-free 0.229 |
| 7PI4 FAK Protac GSK215 in complex with FAK and pVHL:ElonginC:ElonginB Deposited 2021-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain AAA
59–213（155 aa）
|
Not recorded | 7QB (2S,4R)-4-hydroxy-1-((S)-2-(2-(4-(3-methoxy-4-((4-((2-(methylcarbamoyl)phenyl)amino)-5-(trifluoromethyl)pyridin-2-yl)amino)phenyl)piperazin-1-yl)acetamido)-3,3-dimethylbutanoyl)-N-((S)-1-(4-(4-methylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 14 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.05M CaCl, 0.1M MES pH 6.5, 45%v/v, PEG200
|
Resolution 2.24 Å R-free 0.251 |
| 7Q2J Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer Deposited 2021-10-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | 8KH N-[5-[4-[[5-[[(2S)-3,3-dimethyl-1-[(2S,4R)-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-5-oxidanylidene-pentyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1H-pyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21% PEG 3350
0.4 M KSCN
0.1 M HEPES 6.8
|
Resolution 2.50 Å R-free 0.293 |
| 7S4E Crystal Structure of ligand ACBi1 in complex with bromodomain of human Smarca2 and pVHL:ElonginC:ElonginB complex Deposited 2021-09-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–213（160 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 7 NA SODIUM ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 87A N-(1-fluorocyclopropane-1-carbonyl)-3-methyl-L-valyl-(4R)-N-{[2-{2-[4-({4-[3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}methyl)phenoxy]ethoxy}-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-4-hydroxy-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.85；277.15 K；0.1 M HEPES, pH 7.85, 13% PEG 3350, 0.2 M sodium formate
|
Resolution 2.25 Å R-free 0.259 |
| 7S4E Crystal Structure of ligand ACBi1 in complex with bromodomain of human Smarca2 and pVHL:ElonginC:ElonginB complex Deposited 2021-09-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 87A N-(1-fluorocyclopropane-1-carbonyl)-3-methyl-L-valyl-(4R)-N-{[2-{2-[4-({4-[3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}methyl)phenoxy]ethoxy}-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-4-hydroxy-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.85；277.15 K；0.1 M HEPES, pH 7.85, 13% PEG 3350, 0.2 M sodium formate
|
Resolution 2.25 Å R-free 0.259 |
| 7Z6L Crystal structure of PROTAC 5 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–213（160 aa）
|
Not recorded | IEI (2~{S},4~{R})-~{N}-[[2-[3-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]propoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；33% (v/v) glycerol ethoxylate, 0.2 M ammonium chloride, 0.1 M HEPES, pH 7.5
|
Resolution 2.24 Å R-free 0.232 |
| 7Z76 Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | IOD IODIDE ION × 7 IFJ (2~{S},4~{R})-~{N}-[(1~{R})-2-[(2~{R})-1-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]propan-2-yl]oxy-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；14.5 % PEG 3350, 0.1 M BIS-TRIS propane pH 5.8, 100 mM sodium iodide
|
Resolution 1.32 Å R-free 0.202 |
| 7Z77 Crystal structure of compound 6 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | IFF (2~{S},4~{R})-~{N}-[(1~{S})-4-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]butyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20 % PEG 3350, 0.1 M BIS_TRIS propane pH 7.5, 200 mM sodium formate
|
Resolution 1.97 Å R-free 0.251 |
| 7ZNT CRYSTAL STRUCTURE OF AT7 IN COMPLEX WITH THE SECOND BROMODOMAIN OF HUMAN BRD4 AND PVHL:ELONGINC:ELONGINB Deposited 2022-04-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | IZR (2~{S},4~{R})-1-[(2~{R})-3-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexylsulfanyl]-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；10% (W/V) PEG 8000, 0.1 M TRIS-HCL (PH
REMARK 280 7.5) AND 0.1 M MGCL2,
|
Resolution 3.00 Å R-free 0.255 |
| 7ZNT CRYSTAL STRUCTURE OF AT7 IN COMPLEX WITH THE SECOND BROMODOMAIN OF HUMAN BRD4 AND PVHL:ELONGINC:ELONGINB Deposited 2022-04-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | IZR (2~{S},4~{R})-1-[(2~{R})-3-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexylsulfanyl]-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；10% (W/V) PEG 8000, 0.1 M TRIS-HCL (PH
REMARK 280 7.5) AND 0.1 M MGCL2,
|
Resolution 3.00 Å R-free 0.255 |
| 8BB2 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #2) Deposited 2022-10-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
54–213（160 aa）
|
Not recorded | SCN THIOCYANATE ION × 5 Q3X ~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-28% PEG 3350 0.4-1 M KSCN 0.1 M HEPES 6.8
|
Resolution 2.05 Å R-free 0.237 |
| 8BB3 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1) Deposited 2022-10-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
54–213（160 aa）
|
Not recorded | SCN THIOCYANATE ION × 15 EDO 1,2-ETHANEDIOL × 13 P6G HEXAETHYLENE GLYCOL × 1 Q3X ~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-26% PEG 3350 0.4-1 M KSCN 0.1 M HEPES
|
Resolution 1.80 Å R-free 0.227 |
| 8BB4 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 linker Deposited 2022-10-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
54–213（160 aa）
|
Not recorded | Q3R ~{N}-[5-[4-[[4-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-4-oxidanylidene-butyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-28% PEG 3350 0.4 M KSCN 0.1 M HEPES pH 6.8
|
Resolution 2.80 Å R-free 0.279 |
| 8BB5 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker Deposited 2022-10-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | SCN THIOCYANATE ION × 10 Q43 ~{N}-[5-[4-[[4-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethyl]phenyl]methylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG 3350, 0.4-1 M KSCN 0.1 M HEPES pH 6.8
|
Resolution 2.20 Å R-free 0.248 |
| 8BDI VCB in complex with compound 32 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QF7 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-3-(methylamino)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1mM compound soak
|
Resolution 2.11 Å R-free 0.270 |
| 8BDI VCB in complex with compound 32 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QF7 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-3-(methylamino)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1mM compound soak
|
Resolution 2.11 Å R-free 0.270 |
| 8BDI VCB in complex with compound 32 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QF7 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-3-(methylamino)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1mM compound soak
|
Resolution 2.11 Å R-free 0.270 |
| 8BDI VCB in complex with compound 32 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QF7 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-3-(methylamino)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1mM compound soak
|
Resolution 2.11 Å R-free 0.270 |
| 8BDJ VCB in complex with compound 30 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QE0 (2~{S},4~{R})-~{N}-[(1~{S})-1-[4-chloranyl-2-(2-methoxyethoxy)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1 mM Compound soak
|
Resolution 2.02 Å R-free 0.239 |
| 8BDJ VCB in complex with compound 30 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QE0 (2~{S},4~{R})-~{N}-[(1~{S})-1-[4-chloranyl-2-(2-methoxyethoxy)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1 mM Compound soak
|
Resolution 2.02 Å R-free 0.239 |
| 8BDJ VCB in complex with compound 30 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QE0 (2~{S},4~{R})-~{N}-[(1~{S})-1-[4-chloranyl-2-(2-methoxyethoxy)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1 mM Compound soak
|
Resolution 2.02 Å R-free 0.239 |
| 8BDJ VCB in complex with compound 30 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QE0 (2~{S},4~{R})-~{N}-[(1~{S})-1-[4-chloranyl-2-(2-methoxyethoxy)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1 mM Compound soak
|
Resolution 2.02 Å R-free 0.239 |
| 8BDL VCB in complex with compound 27 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QF3 (2~{S},4~{R})-~{N}-[(1~{S})-1-[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, compound soaked at 1mM
|
Resolution 2.29 Å R-free 0.275 |
| 8BDL VCB in complex with compound 27 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QF3 (2~{S},4~{R})-~{N}-[(1~{S})-1-[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, compound soaked at 1mM
|
Resolution 2.29 Å R-free 0.275 |
| 8BDL VCB in complex with compound 27 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QF3 (2~{S},4~{R})-~{N}-[(1~{S})-1-[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, compound soaked at 1mM
|
Resolution 2.29 Å R-free 0.275 |
| 8BDL VCB in complex with compound 27 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QF3 (2~{S},4~{R})-~{N}-[(1~{S})-1-[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, compound soaked at 1mM
|
Resolution 2.29 Å R-free 0.275 |
| 8BDM VCB in complex with compound 26 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QE9 (2~{S},4~{R})-~{N}-[[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound
|
Resolution 2.02 Å R-free 0.255 |
| 8BDM VCB in complex with compound 26 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QE9 (2~{S},4~{R})-~{N}-[[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound
|
Resolution 2.02 Å R-free 0.255 |
| 8BDM VCB in complex with compound 26 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QE9 (2~{S},4~{R})-~{N}-[[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound
|
Resolution 2.02 Å R-free 0.255 |
| 8BDM VCB in complex with compound 26 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QE9 (2~{S},4~{R})-~{N}-[[2-(2-methoxyethoxy)-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound
|
Resolution 2.02 Å R-free 0.255 |
| 8BDN VCB in complex with compound 23 Deposited 2022-10-19 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QFR (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound
|
Resolution 2.76 Å R-free 0.263 |
| 8BDN VCB in complex with compound 23 Deposited 2022-10-19 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QFR (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound
|
Resolution 2.76 Å R-free 0.263 |
| 8BDN VCB in complex with compound 23 Deposited 2022-10-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | QFR (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound
|
Resolution 2.76 Å R-free 0.263 |
| 8BDN VCB in complex with compound 23 Deposited 2022-10-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | QFR (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, soaked with 1mM compound
|
Resolution 2.76 Å R-free 0.263 |
| 8BDO VCB in complex with compound 21 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QFF (2~{S},4~{R})-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-~{N}-[4-(4-methyl-1,3-thiazol-5-yl)phenoxy]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1mM Compound soak
|
Resolution 2.80 Å R-free 0.321 |
| 8BDO VCB in complex with compound 21 Deposited 2022-10-19 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | QFF (2~{S},4~{R})-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-~{N}-[4-(4-methyl-1,3-thiazol-5-yl)phenoxy]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10-20% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate pH 6.5, 1mM Compound soak
|
Resolution 2.80 Å R-free 0.321 |
| 8BDS Ternary complex between VCB, BRD4-BD1 and PROTAC 48 Deposited 2022-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 6 QIY (2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；1.4M Ammonium Sulfate, 4% (w/v) glycerol, 0.1M HEPES pH 7.5
|
Resolution 1.72 Å R-free 0.197 |
| 8BDT Ternary complex between VCB, BRD4-BD2 and PROTAC 51 Deposited 2022-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
54–213（160 aa）
|
Not recorded | QLX (2~{S},4~{R})-~{N}-[(1~{S})-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2M sodium malonate dibasic monohydrate, 20% (w/v) PEG 3350
|
Resolution 2.70 Å R-free 0.243 |
| 8BDT Ternary complex between VCB, BRD4-BD2 and PROTAC 51 Deposited 2022-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
54–213（160 aa）
|
Not recorded | QLX (2~{S},4~{R})-~{N}-[(1~{S})-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 MLI MALONATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2M sodium malonate dibasic monohydrate, 20% (w/v) PEG 3350
|
Resolution 2.70 Å R-free 0.243 |
| 8BDX Ternary complex between VCB, BRD4-BD2 and PROTAC 48 Deposited 2022-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
54–213（160 aa）
|
Not recorded | QIY (2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.02M sodium/potassium phosphate, 0.1M bis-Tris propane pH 7.5
|
Resolution 2.93 Å R-free 0.258 |
| 8BDX Ternary complex between VCB, BRD4-BD2 and PROTAC 48 Deposited 2022-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
54–213（160 aa）
|
Not recorded | QIY (2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.02M sodium/potassium phosphate, 0.1M bis-Tris propane pH 7.5
|
Resolution 2.93 Å R-free 0.258 |
| 8BEB Ternary complex between VCB, BRD4-BD1 and PROTAC 49 Deposited 2022-10-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | SO4 SULFATE ION × 1 QIK (2~{S},4~{R})-~{N}-[(1~{S})-3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]butylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；1.8M ammonium sulfate, 4% (w/v) glycerol, 0.1M bis-Tris pH5.5
|
Resolution 3.18 Å R-free 0.274 |
| 8C13 Crystal structure of pVHL:ElonginC:ElonginB complex bound to PROTAC JW48 Deposited 2022-12-20 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
1–160（160 aa）
|
Not recorded | SYF (2~{S},4~{R})-1-[(2~{S})-2-[3-[2-[2-[2-(acetamidomethyl)-4-(6,7-dihydro-5~{H}-pyrrolo[1,2-a]imidazol-2-yl)phenoxy]ethoxy]ethoxy]propanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；18% PEG 3350, HEPES pH7
|
Resolution 2.30 Å R-free 0.261 |
| 8CQE pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-((S)-1-(2-methyl-4-(4-methylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamide (Compound 37) Deposited 2023-03-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | VFO (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-7-fluoranyl-6-(4-methyl-1,3-thiazol-5-yl)-1,2,3,4-tetrahydronaphthalen-1-yl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate, pH 6.0-6.3, 15-20% polyethylene glycol 3350, 0.2 M magnesium acetate, 10 mM DTT
|
Resolution 2.85 Å R-free 0.297 |
| 8CQE pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-((S)-1-(2-methyl-4-(4-methylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamide (Compound 37) Deposited 2023-03-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | VFO (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-7-fluoranyl-6-(4-methyl-1,3-thiazol-5-yl)-1,2,3,4-tetrahydronaphthalen-1-yl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate, pH 6.0-6.3, 15-20% polyethylene glycol 3350, 0.2 M magnesium acetate, 10 mM DTT
|
Resolution 2.85 Å R-free 0.297 |
| 8CQE pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-((S)-1-(2-methyl-4-(4-methylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamide (Compound 37) Deposited 2023-03-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | VFO (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-7-fluoranyl-6-(4-methyl-1,3-thiazol-5-yl)-1,2,3,4-tetrahydronaphthalen-1-yl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate, pH 6.0-6.3, 15-20% polyethylene glycol 3350, 0.2 M magnesium acetate, 10 mM DTT
|
Resolution 2.85 Å R-free 0.297 |
| 8CQE pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-((S)-1-(2-methyl-4-(4-methylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamide (Compound 37) Deposited 2023-03-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | VFO (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-7-fluoranyl-6-(4-methyl-1,3-thiazol-5-yl)-1,2,3,4-tetrahydronaphthalen-1-yl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate, pH 6.0-6.3, 15-20% polyethylene glycol 3350, 0.2 M magnesium acetate, 10 mM DTT
|
Resolution 2.85 Å R-free 0.297 |
| 8CQK pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-((S)-1-(2-methyl-4-(4-methylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamide (Compound 30) Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain C
54–213（160 aa）
Chain F
54–213（160 aa）
Chain I
54–213（160 aa）
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | VYQ (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-[2-methyl-4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate, 15-20% polyethylene glycol 3350, 0.2 M magnesium acetate,10 mM DTT
|
Resolution 2.62 Å R-free 0.290 |
| 8CQL pVHL:EloB:EloC in complex with (2S,4R)-N-((S)-1-(5-Fluoro-2-methoxy-4-(4-methylthiazol-5-yl)phenyl)ethyl)-1-((S)-2-(1-fluorocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxypyrrolidine-2-carboxamide (Compound 33) Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain C
54–213（160 aa）
Chain F
54–213（160 aa）
Chain I
54–213（160 aa）
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | VH3 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-[5-fluoranyl-2-methoxy-4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；15-20% polyethylene glycol 3350, 0.2 M magnesium acetate, 10 mM DTT
|
Resolution 2.38 Å R-free 0.275 |
| 8EI3 Crystal structure of VHL in complex with H313, a Helicon Polypeptide Deposited 2022-09-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1M Tris pH7.0, 20% w/v PEG 1000
|
Resolution 3.49 Å R-free 0.285 |
| 8EI3 Crystal structure of VHL in complex with H313, a Helicon Polypeptide Deposited 2022-09-14 | Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1M Tris pH7.0, 20% w/v PEG 1000
|
Resolution 3.49 Å R-free 0.285 |
| 8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
|
Resolution 3.40 Å R-free 0.324 |
| 8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
54–213（160 aa）
|
Not recorded | X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
|
Resolution 3.40 Å R-free 0.324 |
| 8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain K
54–213（160 aa）
|
Not recorded | X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
|
Resolution 3.40 Å R-free 0.324 |
| 8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain O
54–213（160 aa）
|
Not recorded | X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
|
Resolution 3.40 Å R-free 0.324 |
| 8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain S
54–213（160 aa）
|
Not recorded | X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
|
Resolution 3.40 Å R-free 0.324 |
| 8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain W
54–213（160 aa）
|
Not recorded | X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
|
Resolution 3.40 Å R-free 0.324 |
| 8FY0 E3:PROTAC:target ternary complex structure (VCB/753b/BCL-xL) Deposited 2023-01-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
54–213（160 aa）
|
Not recorded | CAD CACODYLIC ACID × 1 GOL GLYCEROL × 2 YF8 N-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.1 M Sodium Cacodylate pH 5.5, 0.2 M Sodium chloride, 6-8% PEG 8000 and 4% tert-Butanediol
|
Resolution 2.94 Å R-free 0.241 |
| 8FY1 E3:PROTAC:target ternary complex structure (VCB/753b/BCL-2) Deposited 2023-01-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
54–213（160 aa）
|
Not recorded | YF8 N-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.1 M Tris-Cl pH 8.7, 18% PEG 8000, 0.2 M MgCl2 and 3% 1,6-Hexanediol
|
Resolution 2.56 Å R-free 0.250 |
| 8FY2 E3:PROTAC:target ternary complex structure (VCB/WH244/BCL-2) Deposited 2023-01-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
54–213（160 aa）
|
Not recorded | YFH N-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.1 M Tris-Cl pH 8.7, 18% PEG 8000, 0.2 M MgCl2 and 3% 1,6-Hexanediol
|
Resolution 2.98 Å R-free 0.279 |
| 8G1P Co-crystal structure of Compound 11 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2023-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
56–213（158 aa）
|
Not recorded | GOL GLYCEROL × 1 FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；20% PEG 3350, 0.2M Sodium Chloride
|
Resolution 2.70 Å R-free 0.270 |
| 8G1P Co-crystal structure of Compound 11 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2023-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
56–213（158 aa）
|
Not recorded | GOL GLYCEROL × 1 FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；20% PEG 3350, 0.2M Sodium Chloride
|
Resolution 2.70 Å R-free 0.270 |
| 8G1Q Co-crystal structure of Compound 1 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB Deposited 2023-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
56–213（158 aa）
|
Not recorded | NA SODIUM ION × 1 YHB N-(2-{4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}pyridine-4-carbonyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；PEG 300
0.1M Bis-Tris 6.5
|
Resolution 3.73 Å R-free 0.326 |
| 8P0F Crystal structure of the VCB complex with compound 1. Deposited 2023-05-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
54–213（160 aa）
|
Not recorded | WBN (3~{R},5~{R})-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-5-oxidanyl-2-oxidanylidene-1-pyridin-2-yl-piperidine-3-carboxamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30 % PEG
|
Resolution 1.98 Å R-free 0.257 |
| 8P0F Crystal structure of the VCB complex with compound 1. Deposited 2023-05-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
54–213（160 aa）
|
Not recorded | WBN (3~{R},5~{R})-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-5-oxidanyl-2-oxidanylidene-1-pyridin-2-yl-piperidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30 % PEG
|
Resolution 1.98 Å R-free 0.257 |
| 8PC2 SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC Deposited 2023-06-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–213（160 aa）
|
Not recorded | XZW [(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl] (2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；15% PEG3350, 0.2 M tri-sodium citrate, 0.1 M HEPES-NaOH pH 7.5 and 10% glycol
|
Resolution 2.80 Å R-free 0.261 |
| 8PC2 SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC Deposited 2023-06-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
54–213（160 aa）
|
Not recorded | XZW [(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl] (2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；15% PEG3350, 0.2 M tri-sodium citrate, 0.1 M HEPES-NaOH pH 7.5 and 10% glycol
|
Resolution 2.80 Å R-free 0.261 |
| 8QJR BRG1 bromodomain in complex with VBC via compound 17 Deposited 2023-09-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | PO4 PHOSPHATE ION × 5 GOL GLYCEROL × 1 VLH (2S,4R)-1-[(2R)-2-[3-[2-[4-[3-[4-[(1R,5S)-3-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]pyridin-2-yl]oxycyclobutyl]oxypiperidin-1-yl]ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；27 mM HEPES pH 6.8, 73 mM HEPES pH 8.6, 1.0 M NaI
|
Resolution 3.17 Å R-free 0.278 |
| 8QJR BRG1 bromodomain in complex with VBC via compound 17 Deposited 2023-09-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | PO4 PHOSPHATE ION × 2 VLH (2S,4R)-1-[(2R)-2-[3-[2-[4-[3-[4-[(1R,5S)-3-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]pyridin-2-yl]oxycyclobutyl]oxypiperidin-1-yl]ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；27 mM HEPES pH 6.8, 73 mM HEPES pH 8.6, 1.0 M NaI
|
Resolution 3.17 Å R-free 0.278 |
| 8QJS VHL/Elongin B/Elongin C complex with compound 155 Deposited 2023-09-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Not recorded | VL6 (2S,4R)-1-[(2R)-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 3.19 Å R-free 0.274 |
| 8QJS VHL/Elongin B/Elongin C complex with compound 155 Deposited 2023-09-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Not recorded | VL6 (2S,4R)-1-[(2R)-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 3.19 Å R-free 0.274 |
| 8QJS VHL/Elongin B/Elongin C complex with compound 155 Deposited 2023-09-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Not recorded | VL6 (2S,4R)-1-[(2R)-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 3.19 Å R-free 0.274 |
| 8QJS VHL/Elongin B/Elongin C complex with compound 155 Deposited 2023-09-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Not recorded | VL6 (2S,4R)-1-[(2R)-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 3.19 Å R-free 0.274 |
| 8QU8 PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1 Deposited 2023-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
2–213（212 aa）
|
Not recorded | ZN ZINC ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 WYL (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8QVU Crystal Structure of ligand ACBI3 in complex with KRAS G12D C118S GDP and pVHL:ElonginC:ElonginB complex Deposited 2023-10-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
1–213（213 aa）
|
Not recorded | WYL (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；20% w/v PEG 8000, 0.2 M lithium chloride, 0.1 M Tris pH 8.0
|
Resolution 2.24 Å R-free 0.287 |
| 8QVU Crystal Structure of ligand ACBI3 in complex with KRAS G12D C118S GDP and pVHL:ElonginC:ElonginB complex Deposited 2023-10-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–213（213 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 WYL (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；20% w/v PEG 8000, 0.2 M lithium chloride, 0.1 M Tris pH 8.0
|
Resolution 2.24 Å R-free 0.287 |
| 8QW6 Crystal Structure of compound 3 in complex with KRAS G12V C118S GDP and pVHL:ElonginC:ElonginB Deposited 2023-10-18 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Mutation：Delta 1-53 | GDP GUANOSINE-5'-DIPHOSPHATE × 1 X4R (2S,4R)-1-[(2S)-2-[6-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]hexanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；200 mM sodium citrate, 100 mM BIS-TRIS propane pH 8.5, 20% w/v polyethylene glycol 3350
|
Resolution 2.20 Å R-free 0.295 |
| 8QW6 Crystal Structure of compound 3 in complex with KRAS G12V C118S GDP and pVHL:ElonginC:ElonginB Deposited 2023-10-18 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–213（160 aa）
|
Mutation：Delta 1-53 | GDP GUANOSINE-5'-DIPHOSPHATE × 1 X4R (2S,4R)-1-[(2S)-2-[6-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]hexanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；200 mM sodium citrate, 100 mM BIS-TRIS propane pH 8.5, 20% w/v polyethylene glycol 3350
|
Resolution 2.20 Å R-free 0.295 |
| 8QW7 Crystal Structure of compound 4 in complex with KRAS G12V C118S GDP and pVHL:ElonginC:ElonginB Deposited 2023-10-18 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–213（160 aa）
|
Mutation：Delta 1-53 | X53 (2S,4R)-1-[(2R)-2-[3-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；200 mM Lithium sulfate monohydrate, 100 mM BIS-TRIS propane pH 5.5, 25% w/v polyethylene glycol 3350
|
Resolution 2.36 Å R-free 0.273 |
| 8QW7 Crystal Structure of compound 4 in complex with KRAS G12V C118S GDP and pVHL:ElonginC:ElonginB Deposited 2023-10-18 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Mutation：Delta 1-53 | X53 (2S,4R)-1-[(2R)-2-[3-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；200 mM Lithium sulfate monohydrate, 100 mM BIS-TRIS propane pH 5.5, 25% w/v polyethylene glycol 3350
|
Resolution 2.36 Å R-free 0.273 |
| 8R5H Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 Deposited 2023-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain H
1–160（160 aa）
|
Not recorded | ZN ZINC ION × 3 SY8 5-azanylpentan-2-one × 1 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.44 Å |
| 8RWZ Open non-crosslinked structure Brd4BD2-MZ1-(NEDD8)-CRL2VHL Deposited 2024-02-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–160（160 aa）
|
Not recorded | 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain B
1–160（160 aa）
|
Not recorded | 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8VL9 Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue Deposited 2024-01-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
54–213（160 aa）
|
Not recorded | A1ACI N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide × 1 CIT CITRIC ACID × 1 FE2 FE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.2M SODIUM CITRATE, 0.1M BIS-TRIS-PROPANE PH 6.5, 20% PEG3350
|
Resolution 2.50 Å R-free 0.216 |
| 8VLB Crystal structure of EloBC-VHL-CDO1 complex bound to compound 4 molecular glue Deposited 2024-01-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
54–213（160 aa）
|
Not recorded | 3JF N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 CIT CITRIC ACID × 1 FE2 FE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.2M SODIUM CITRATE, 0.1M BIS-TRIS-PROPANE PH 6.5, 20% PEG3350
|
Resolution 2.90 Å R-free 0.258 |
| 8WDK The complex structure of Cul2-VCB-Protac-Wee1 Deposited 2023-09-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain V
59–213（155 aa）
|
Not recorded | W6U (2S,4R)-1-[(2S)-3,3-dimethyl-2-[3-[4-[4-[4-[[3-oxidanylidene-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]-2-prop-2-enyl-pyrazolo[3,4-d]pyrimidin-6-yl]amino]phenyl]piperazin-1-yl]butoxy]propanoylamino]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.64 Å |
| 8YMB The crystal structure of SHD931 in complex with Brd4-BD2 and VCB Deposited 2024-03-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
55–213（159 aa）
|
Not recorded | CL CHLORIDE ION × 5 A1LY0 SHD931 × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；1500 mM Ammonium sulfate, 100 mM Tris base/ Hydrochloric acid, pH 8.5, 12% (v/v) Glycerol
|
Resolution 2.95 Å R-free 0.270 |
| 8YMB The crystal structure of SHD931 in complex with Brd4-BD2 and VCB Deposited 2024-03-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
55–213（159 aa）
|
Not recorded | CL CHLORIDE ION × 3 A1LY0 SHD931 × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；1500 mM Ammonium sulfate, 100 mM Tris base/ Hydrochloric acid, pH 8.5, 12% (v/v) Glycerol
|
Resolution 2.95 Å R-free 0.270 |
| 8ZV8 Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_2 (D7) Deposited 2024-06-11 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1L2C 4-(hydroxymethyl)-7-oxidanyl-chromen-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT
|
Resolution 2.46 Å R-free 0.287 |
| 8ZV8 Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_2 (D7) Deposited 2024-06-11 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1L2C 4-(hydroxymethyl)-7-oxidanyl-chromen-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT
|
Resolution 2.46 Å R-free 0.287 |
| 8ZV8 Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_2 (D7) Deposited 2024-06-11 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1L2C 4-(hydroxymethyl)-7-oxidanyl-chromen-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT
|
Resolution 2.46 Å R-free 0.287 |
| 8ZV8 Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_2 (D7) Deposited 2024-06-11 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1L2C 4-(hydroxymethyl)-7-oxidanyl-chromen-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT
|
Resolution 2.46 Å R-free 0.287 |
| 8ZVJ Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_1(DE22) Deposited 2024-06-11 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1L2D ethyl 7-oxidanyl-2-oxidanylidene-chromene-4-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT
|
Resolution 2.60 Å R-free 0.285 |
| 8ZVJ Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_1(DE22) Deposited 2024-06-11 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT
|
Resolution 2.60 Å R-free 0.285 |
| 8ZVJ Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_1(DE22) Deposited 2024-06-11 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1L2D ethyl 7-oxidanyl-2-oxidanylidene-chromene-4-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT
|
Resolution 2.60 Å R-free 0.285 |
| 8ZVJ Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_1(DE22) Deposited 2024-06-11 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1L2D ethyl 7-oxidanyl-2-oxidanylidene-chromene-4-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT
|
Resolution 2.60 Å R-free 0.285 |
| 9BJU Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5 Deposited 2024-04-25 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | TFA trifluoroacetic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT
|
Resolution 2.47 Å R-free 0.256 |
| 9BJU Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5 Deposited 2024-04-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT
|
Resolution 2.47 Å R-free 0.256 |
| 9BJU Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5 Deposited 2024-04-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
54–213（160 aa）
|
Not recorded | ACT ACETATE ION × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT
|
Resolution 2.47 Å R-free 0.256 |
| 9BJU Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5 Deposited 2024-04-25 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | TFA trifluoroacetic acid × 1 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT
|
Resolution 2.47 Å R-free 0.256 |
| 9BOL Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5 Deposited 2024-05-03 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 1 A1ARP (4R)-1-[(2S)-2-(4-cyclopropyl-1H-1,2,3-triazol-1-yl)-3,3-dimethylbutanoyl]-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT
|
Resolution 1.99 Å R-free 0.248 |
| 9BOL Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5 Deposited 2024-05-03 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 1 A1ARP (4R)-1-[(2S)-2-(4-cyclopropyl-1H-1,2,3-triazol-1-yl)-3,3-dimethylbutanoyl]-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT
|
Resolution 1.99 Å R-free 0.248 |
| 9D4B Discovery of SMD-3236, a Potent, Highly Selective and Efficacious SMARCA2 Degrader for the Treatment of SMARC4-Deficient Human Cancers Deposited 2024-08-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
54–213（160 aa）
|
Not recorded | A1A1U (4R)-1-[(2S)-2-{4-[(1S,4S)-4-({4-[(12'S)-4'-chloro-5'-oxo-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-10'-yl]piperidin-1-yl}methyl)cyclohexyl]-1H-1,2,3-triazol-1-yl}-3,3-dimethylbutanoyl]-4-hydroxy-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-(morpholin-4-yl)ethyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；281.15 K；0.25 M Calcium acetate
0.1 M Sodium cacodylate pH 5.5
8% w/v PEG 8000
|
Resolution 3.30 Å R-free 0.286 |
| 9D4B Discovery of SMD-3236, a Potent, Highly Selective and Efficacious SMARCA2 Degrader for the Treatment of SMARC4-Deficient Human Cancers Deposited 2024-08-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
54–213（160 aa）
|
Not recorded | A1A1U (4R)-1-[(2S)-2-{4-[(1S,4S)-4-({4-[(12'S)-4'-chloro-5'-oxo-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-10'-yl]piperidin-1-yl}methyl)cyclohexyl]-1H-1,2,3-triazol-1-yl}-3,3-dimethylbutanoyl]-4-hydroxy-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-(morpholin-4-yl)ethyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；281.15 K；0.25 M Calcium acetate
0.1 M Sodium cacodylate pH 5.5
8% w/v PEG 8000
|
Resolution 3.30 Å R-free 0.286 |
| 9DTX Crystal structure of PRT3789 in complex with the bromodomain of human BRG1 (SMARCA4) and pVHL:ElonginC:ElonginB Deposited 2024-10-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
Fragment：UNP residues 54-213
|
Not recorded | A1BB4 (4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Bis-Tris propane, pH 8.5, 0.2 M potassium thiocyanate, 20% w/v PEG3350
|
Resolution 2.11 Å R-free 0.232 |
| 9DTY Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2024-10-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric |
Chain B
54–213（160 aa）
Fragment：UNP residues 54-213
Chain F
54–213（160 aa）
Fragment：UNP residues 54-213
Chain J
54–213（160 aa）
Fragment：UNP residues 54-213
Chain N
54–213（160 aa）
Fragment：UNP residues 54-213
Chain R
54–213（160 aa）
Fragment：UNP residues 54-213
Chain V
54–213（160 aa）
Fragment：UNP residues 54-213
Chain Z
54–213（160 aa）
Fragment：UNP residues 54-213
Chain d
54–213（160 aa）
Fragment：UNP residues 54-213
Chain h
54–213（160 aa）
Fragment：UNP residues 54-213
Chain l
54–213（160 aa）
Fragment：UNP residues 54-213
|
Not recorded | A1BB4 (4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 10 CIT CITRIC ACID × 5 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.26；291 K；2% v/v Tacsimate, pH 5.0, 0.1 M tri-sodium citrate, pH 5.26, 11.36% w/v PEG3350, 0.1 M barium chloride dihydrate
|
Resolution 3.19 Å R-free 0.285 |
| 9EQJ Crystal structure of pVHL:EloB:EloC in complex with MP-1-39 Deposited 2024-03-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Not recorded | A1H6O (2S,4R)-1-[(2R)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-3-[[cis-4-(morpholin-4-ylmethyl)cyclohexyl]methylsulfanyl]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 NaCl, 0.1M HEPES pH 7.5, and 25% PEG3350
|
Resolution 2.05 Å R-free 0.216 |
| 9EQJ Crystal structure of pVHL:EloB:EloC in complex with MP-1-39 Deposited 2024-03-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Not recorded | A1H6O (2S,4R)-1-[(2R)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-3-[[cis-4-(morpholin-4-ylmethyl)cyclohexyl]methylsulfanyl]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 NaCl, 0.1M HEPES pH 7.5, and 25% PEG3350
|
Resolution 2.05 Å R-free 0.216 |
| 9EQM Crystal structure of pVHL:EloB:EloC in complex with MP-1-21 Deposited 2024-03-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Not recorded | A1H9F (2S,4R)-1-[(2R)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-3-[[trans-4-(morpholin-4-ylmethyl)cyclohexyl]methylsulfanyl]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.285 M sodium acetate, 0.1M Bis-Tris pH 5.5, and 5.9% PEG3350
|
Resolution 2.19 Å R-free 0.264 |
| 9GIO Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of VHL. Deposited 2024-08-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–160（160 aa）
|
Not recorded | 3JF N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 A1IMD N-[2-(dimethylsulfamoyl)-5-[(1-methylpyrazol-4-yl)methoxy]phenyl]propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；12 % PEG8000 and 100 mM MES buffer (pH 6.5).
|
Resolution 1.49 Å R-free 0.233 |
| 9H30 VHL:ElonginC:ElonginB-PROTAC4 complex Deposited 2024-10-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
54–213（160 aa）
|
Not recorded | A1ISE N-[5-(1-{2-[4-({[(1S,2R,3S,5S,6S,16E,18E,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl]oxy}carbonyl)phenyl]ethyl}-1H-1,2,3-triazol-4-yl)pentanoyl]-3-methyl-D-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；277 K；9-11% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate, pH 5.7
|
Resolution 2.50 Å R-free 0.250 |
| 9HYB CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3 Deposited 2025-01-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | A1IYB (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris propane, 20 % PEG 3350, 0.2 M tri-sodium citrate
|
Resolution 2.84 Å R-free 0.265 |
| 9HYB CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3 Deposited 2025-01-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | A1IYB (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris propane, 20 % PEG 3350, 0.2 M tri-sodium citrate
|
Resolution 2.84 Å R-free 0.265 |
| 9HYB CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3 Deposited 2025-01-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
54–213（160 aa）
|
Not recorded | A1IYB (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris propane, 20 % PEG 3350, 0.2 M tri-sodium citrate
|
Resolution 2.84 Å R-free 0.265 |
| 9HYB CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3 Deposited 2025-01-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
54–213（160 aa）
|
Not recorded | A1IYB (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris propane, 20 % PEG 3350, 0.2 M tri-sodium citrate
|
Resolution 2.84 Å R-free 0.265 |
| 9HYN CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P1 Deposited 2025-01-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | A1IYO (2~{S},4~{R})-~{N}-[[2-[2-[2-[4-[(6-bromanyl-3-methyl-5-oxidanylidene-4~{H}-imidazo[1,2-a]quinazolin-2-yl)methyl]piperazin-1-yl]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M K2HPO4
16 % PEG 8000
0.2 M sodium chloride
|
Resolution 2.37 Å R-free 0.262 |
| 9HYN CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P1 Deposited 2025-01-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | A1IYO (2~{S},4~{R})-~{N}-[[2-[2-[2-[4-[(6-bromanyl-3-methyl-5-oxidanylidene-4~{H}-imidazo[1,2-a]quinazolin-2-yl)methyl]piperazin-1-yl]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M K2HPO4
16 % PEG 8000
0.2 M sodium chloride
|
Resolution 2.37 Å R-free 0.262 |
| 9HYO CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P4 Deposited 2025-01-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
54–213（160 aa）
|
Not recorded | A1IYN (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[7-(5-bromanyl-4-oxidanylidene-2,3-dihydro-1,3-benzoxazin-2-yl)-4-[cyclopropyl(methyl)amino]-5,6,8,9-tetrahydropyrimido[4,5-d]azepin-2-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES pH 7.0
8% ethylene glycol
14% PEG 8K
|
Resolution 3.74 Å R-free 0.348 |
| 9HYP CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P5 Deposited 2025-01-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
54–213（160 aa）
|
Not recorded | A1IYM (2~{S},4~{R})-~{N}-[[2-[4-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]butoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；28% PEG 3350
0.2 M potassium thiocyanate
0.1 M Bis-Tris Propane pH 7.5
|
Resolution 2.20 Å R-free 0.254 |
| 9IPW Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_5(D3) Deposited 2024-07-11 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K,0.1M Na cacodylate-HCl pH 6.0, 0.2M Mg acetate, 5mM DTT
|
Resolution 3.00 Å R-free 0.273 |
| 9IPW Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_5(D3) Deposited 2024-07-11 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K,0.1M Na cacodylate-HCl pH 6.0, 0.2M Mg acetate, 5mM DTT
|
Resolution 3.00 Å R-free 0.273 |
| 9IPW Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_5(D3) Deposited 2024-07-11 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K,0.1M Na cacodylate-HCl pH 6.0, 0.2M Mg acetate, 5mM DTT
|
Resolution 3.00 Å R-free 0.273 |
| 9IPW Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_5(D3) Deposited 2024-07-11 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1L2Z 7-Hydroxy-4-methoxymethylcoumarin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；12% PEG 8K,0.1M Na cacodylate-HCl pH 6.0, 0.2M Mg acetate, 5mM DTT
|
Resolution 3.00 Å R-free 0.273 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–213（160 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
54–213（160 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain J
54–213（160 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain N
54–213（160 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain R
54–213（160 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
54–213（160 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain Z
54–213（160 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain d
54–213（160 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9N88 PROTAC-induced IRE1 ternary complex Deposited 2025-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain B
61–207（147 aa）
Chain F
61–207（147 aa）
|
Not recorded | A1BWF 3-methyl-N-(5-{4-[(1r,4S)-4-{[7-oxo-8-(propan-2-yl)-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}cyclohexyl]piperazin-1-yl}pentanoyl)-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2；I used 0.5 mM BS3 for crosslinking the protein complex, then diluted it to 0.05 mM for grid preparation.
cryo-EM vitrification conditions
Cryogen ETHANE；7 force; 2 s blot time.
|
Resolution 2.60 Å |
| 9OIM The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 9 Deposited 2025-05-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1CBI 1-[5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.61 Å R-free 0.283 |
| 9OIM The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 9 Deposited 2025-05-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1CBI 1-[5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.61 Å R-free 0.283 |
| 9OIM The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 9 Deposited 2025-05-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1CBI 1-[5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.61 Å R-free 0.283 |
| 9OIM The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 9 Deposited 2025-05-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1CBI 1-[5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.61 Å R-free 0.283 |
| 9OIN The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 13 Deposited 2025-05-06 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.41 Å R-free 0.283 |
| 9OIN The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 13 Deposited 2025-05-06 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.41 Å R-free 0.283 |
| 9OIN The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 13 Deposited 2025-05-06 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.41 Å R-free 0.283 |
| 9OIN The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 13 Deposited 2025-05-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1CBJ 1-(propan-2-yl)-4-[(pyridin-2-yl)methyl]piperazine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.41 Å R-free 0.283 |
| 9OIO The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragments 9 and 14 Deposited 2025-05-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1CBL 1-[(2-fluorophenyl)methyl]-4-(propan-2-yl)piperazine × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.30 Å R-free 0.249 |
| 9OIO The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragments 9 and 14 Deposited 2025-05-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1CBL 1-[(2-fluorophenyl)methyl]-4-(propan-2-yl)piperazine × 1 DMS DIMETHYL SULFOXIDE × 2 A1CBK 1-[6-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.30 Å R-free 0.249 |
| 9OIO The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragments 9 and 14 Deposited 2025-05-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 2 A1CBK 1-[6-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.30 Å R-free 0.249 |
| 9OIO The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragments 9 and 14 Deposited 2025-05-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1CBL 1-[(2-fluorophenyl)methyl]-4-(propan-2-yl)piperazine × 1 DMS DIMETHYL SULFOXIDE × 1 A1CBK 1-[6-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.30 Å R-free 0.249 |
| 9OIQ The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 15 Deposited 2025-05-06 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.66 Å R-free 0.275 |
| 9OIQ The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 15 Deposited 2025-05-06 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.66 Å R-free 0.275 |
| 9OIQ The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 15 Deposited 2025-05-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Not recorded | A1CBM 2-(5-amino-1H-1,3-benzimidazol-1-yl)ethan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.66 Å R-free 0.275 |
| 9OIQ The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 15 Deposited 2025-05-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Not recorded | A1CBM 2-(5-amino-1H-1,3-benzimidazol-1-yl)ethan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000
|
Resolution 2.66 Å R-free 0.275 |
| 9QE4 VCB in complex with VHL-binding compound 114 Deposited 2025-03-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1I57 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；277 K；0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
|
Resolution 2.28 Å R-free 0.301 |
| 9QE4 VCB in complex with VHL-binding compound 114 Deposited 2025-03-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1I57 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；277 K；0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
|
Resolution 2.28 Å R-free 0.301 |
| 9QE4 VCB in complex with VHL-binding compound 114 Deposited 2025-03-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1I57 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；277 K；0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
|
Resolution 2.28 Å R-free 0.301 |
| 9QE4 VCB in complex with VHL-binding compound 114 Deposited 2025-03-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1I57 (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；277 K；0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
|
Resolution 2.28 Å R-free 0.301 |
| 9QE5 VCB in complex with VHL-binding compound 82 Deposited 2025-03-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1I58 (2~{S},4~{R})-1-[(2~{S})-1-(1-fluoranylcyclopropyl)carbonylpiperidin-2-yl]carbonyl-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；277 K；0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
|
Resolution 2.50 Å R-free 0.273 |
| 9QE5 VCB in complex with VHL-binding compound 82 Deposited 2025-03-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1I58 (2~{S},4~{R})-1-[(2~{S})-1-(1-fluoranylcyclopropyl)carbonylpiperidin-2-yl]carbonyl-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；277 K；0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
|
Resolution 2.50 Å R-free 0.273 |
| 9QE5 VCB in complex with VHL-binding compound 82 Deposited 2025-03-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1I58 (2~{S},4~{R})-1-[(2~{S})-1-(1-fluoranylcyclopropyl)carbonylpiperidin-2-yl]carbonyl-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；277 K；0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
|
Resolution 2.50 Å R-free 0.273 |
| 9QE5 VCB in complex with VHL-binding compound 82 Deposited 2025-03-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1I58 (2~{S},4~{R})-1-[(2~{S})-1-(1-fluoranylcyclopropyl)carbonylpiperidin-2-yl]carbonyl-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；277 K；0.1 M sodium cacodylate pH 5.7,
0.2 M magnesium acetate,
12% (w/v) PEG 3350,
5 mM DTT
|
Resolution 2.50 Å R-free 0.273 |
| 9RK8 Crystal Structure of compound 3-mediated ternary complex of KRAS G12V C118S GDP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | A1JH1 (2~{S},4~{R})-1-[(2~{S})-2-[[1-[4-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butanoyl]cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M Tris pH 7.0, 0.2 M MgCl2, 10%w/v PEG 8000
|
Resolution 2.63 Å R-free 0.263 |
| 9RK8 Crystal Structure of compound 3-mediated ternary complex of KRAS G12V C118S GDP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
54–213（160 aa）
|
Not recorded | A1JH1 (2~{S},4~{R})-1-[(2~{S})-2-[[1-[4-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butanoyl]cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M Tris pH 7.0, 0.2 M MgCl2, 10%w/v PEG 8000
|
Resolution 2.63 Å R-free 0.263 |
| 9RKC Crystal Structure of ACBI4-mediated ternary complex of KRAS G12D C118S GDP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | A1JHI (2~{S},4~{R})-1-[(2~{S})-2-[(5~{S})-5-[3-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]propyl]-4,5,6,7-tetrahydrobenzotriazol-1-yl]-3-methyl-butanoyl]-~{N}-[(1-methylindazol-6-yl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Na2SO4, 15% w/v PEG 3,350, 0.1 M BIS-TRIS propane pH 7.79
|
Resolution 2.19 Å R-free 0.275 |
| 9RKC Crystal Structure of ACBI4-mediated ternary complex of KRAS G12D C118S GDP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
54–213（160 aa）
|
Not recorded | A1JHI (2~{S},4~{R})-1-[(2~{S})-2-[(5~{S})-5-[3-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]propyl]-4,5,6,7-tetrahydrobenzotriazol-1-yl]-3-methyl-butanoyl]-~{N}-[(1-methylindazol-6-yl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Na2SO4, 15% w/v PEG 3,350, 0.1 M BIS-TRIS propane pH 7.79
|
Resolution 2.19 Å R-free 0.275 |
| 9RKE Crystal Structure of compound 1-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | GOL GLYCEROL × 1 X53 (2S,4R)-1-[(2R)-2-[3-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M Bis Tris pH 7.3, 0.3 M trisodium citrate, 20% PEG 3350
|
Resolution 2.83 Å R-free 0.286 |
| 9RKE Crystal Structure of compound 1-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
54–213（160 aa）
|
Not recorded | X53 (2S,4R)-1-[(2R)-2-[3-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M Bis Tris pH 7.3, 0.3 M trisodium citrate, 20% PEG 3350
|
Resolution 2.83 Å R-free 0.286 |
| 9RKJ Crystal Structure of compound 3-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | FLC CITRATE ANION × 2 A1JH1 (2~{S},4~{R})-1-[(2~{S})-2-[[1-[4-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butanoyl]cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M Bis Tris pH 7.3, 0.167 M trisodium citrate, 17%(w/v) PEG 3350
|
Resolution 2.89 Å R-free 0.288 |
| 9RKJ Crystal Structure of compound 3-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
54–213（160 aa）
|
Not recorded | A1JH1 (2~{S},4~{R})-1-[(2~{S})-2-[[1-[4-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butanoyl]cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M Bis Tris pH 7.3, 0.167 M trisodium citrate, 17%(w/v) PEG 3350
|
Resolution 2.89 Å R-free 0.288 |
| 9RKN Crystal Structure of ACBI4-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
54–213（160 aa）
|
Not recorded | SO4 SULFATE ION × 3 A1JHI (2~{S},4~{R})-1-[(2~{S})-2-[(5~{S})-5-[3-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]propyl]-4,5,6,7-tetrahydrobenzotriazol-1-yl]-3-methyl-butanoyl]-~{N}-[(1-methylindazol-6-yl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.14 M Ammonium sulfate, 25% w/v Polyethylene glycol 3,350, 0.1M BIS-TRIS pH 5.8
|
Resolution 2.85 Å R-free 0.275 |
| 9RKN Crystal Structure of ACBI4-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB Deposited 2025-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
54–213（160 aa）
|
Not recorded | A1JHI (2~{S},4~{R})-1-[(2~{S})-2-[(5~{S})-5-[3-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]propyl]-4,5,6,7-tetrahydrobenzotriazol-1-yl]-3-methyl-butanoyl]-~{N}-[(1-methylindazol-6-yl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.14 M Ammonium sulfate, 25% w/v Polyethylene glycol 3,350, 0.1M BIS-TRIS pH 5.8
|
Resolution 2.85 Å R-free 0.275 |
| 9SNO VHL/Elongin B/Elongin C complex with compound 59 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Not recorded | A1JO9 (2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[6-(4-methyl-1,3-thiazol-5-yl)pyridin-3-yl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.80 Å R-free 0.298 |
| 9SNO VHL/Elongin B/Elongin C complex with compound 59 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Not recorded | A1JO9 (2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[6-(4-methyl-1,3-thiazol-5-yl)pyridin-3-yl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.80 Å R-free 0.298 |
| 9SNO VHL/Elongin B/Elongin C complex with compound 59 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Not recorded | A1JO9 (2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[6-(4-methyl-1,3-thiazol-5-yl)pyridin-3-yl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.80 Å R-free 0.298 |
| 9SNO VHL/Elongin B/Elongin C complex with compound 59 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Not recorded | A1JO9 (2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[6-(4-methyl-1,3-thiazol-5-yl)pyridin-3-yl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.80 Å R-free 0.298 |
| 9SNP VHL/Elongin B/Elongin C complex with compound 60 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Not recorded | A1JO8 (2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.70 Å R-free 0.259 |
| 9SNP VHL/Elongin B/Elongin C complex with compound 60 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Not recorded | A1JO8 (2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.70 Å R-free 0.259 |
| 9SNP VHL/Elongin B/Elongin C complex with compound 60 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Not recorded | A1JO8 (2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.70 Å R-free 0.259 |
| 9SNP VHL/Elongin B/Elongin C complex with compound 60 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Not recorded | A1JO8 (2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.70 Å R-free 0.259 |
| 9SNQ VHL/Elongin B/Elongin C complex with compound 61 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
54–213（160 aa）
|
Not recorded | A1JO1 (2~{S},4~{R})-~{N}-[(1~{S})-1-(4-cyanophenyl)ethyl]-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.60 Å R-free 0.257 |
| 9SNQ VHL/Elongin B/Elongin C complex with compound 61 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
54–213（160 aa）
|
Not recorded | A1JO1 (2~{S},4~{R})-~{N}-[(1~{S})-1-(4-cyanophenyl)ethyl]-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.60 Å R-free 0.257 |
| 9SNQ VHL/Elongin B/Elongin C complex with compound 61 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
54–213（160 aa）
|
Not recorded | A1JO1 (2~{S},4~{R})-~{N}-[(1~{S})-1-(4-cyanophenyl)ethyl]-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.60 Å R-free 0.257 |
| 9SNQ VHL/Elongin B/Elongin C complex with compound 61 Deposited 2025-09-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
54–213（160 aa）
|
Not recorded | A1JO1 (2~{S},4~{R})-~{N}-[(1~{S})-1-(4-cyanophenyl)ethyl]-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000
|
Resolution 2.60 Å R-free 0.257 |
| 9SV3 Local refinement of EloB/EloC/VHL/CV2a/14-3-3zeta/ERa from pose 1 Deposited 2025-09-30 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain E
54–213（160 aa）
|
Not recorded | A1JQT ~{N}'-[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]-~{N}-[(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl]tridecanediamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 9T32 The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11 Deposited 2025-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain C
62–202（141 aa）
Chain H
62–202（141 aa）
|
Not recorded | A1JTC (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[2-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
141 other PDB entries and 360 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | VHL_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 4–163； UniProt 54–213 Author chain E； PDBConstruct 4–163； UniProt 54–213 Author chain I； PDBConstruct 4–163； UniProt 54–213 Author chain M； PDBConstruct 4–163； UniProt 54–213 |
