Protein VPRBP
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1039–1401 | Mutation：Q1250L | UNX UNKNOWN LIGAND × 22 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；291 K；0.1 M sodium hepes, 0.2 M lithium sulfate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 291K | Resolution 1.72 Å R-free 0.219 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 1039–1401 | Mutation：Q1250L | UNX UNKNOWN LIGAND × 23 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；291 K；0.1 M sodium hepes, 0.2 M lithium sulfate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 291K | Resolution 1.72 Å R-free 0.219 |
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 4PXW | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3WA0 Crystal structure of merlin complexed with DCAF1/VprBP Deposited 2013-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
1417–1506（90 aa）
Fragment：UNP residues 1417-1506
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.31 Å R-free 0.264 |
| 3WA0 Crystal structure of merlin complexed with DCAF1/VprBP Deposited 2013-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
1417–1506（90 aa）
Fragment：UNP residues 1417-1506
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.31 Å R-free 0.264 |
| 4CC9 Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to Vpx isolated from sooty mangabey and human DCAF1 (amino acid residues 1058-1396) Deposited 2013-10-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1058–1396（339 aa）
Fragment：RESIDUES 1058-1396
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.2 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 15% PEG 400
|
Resolution 2.47 Å R-free 0.216 |
| 4P7I Crystal structure of the Merlin FERM/DCAF1 complex Deposited 2014-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
998–1058（61 aa）
Fragment：UNP residues 998-1058
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% Isopropanol and 5% PEG8000
|
Resolution 2.60 Å R-free 0.256 |
| 4P7I Crystal structure of the Merlin FERM/DCAF1 complex Deposited 2014-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
998–1058（61 aa）
Fragment：UNP residues 998-1058
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% Isopropanol and 5% PEG8000
|
Resolution 2.60 Å R-free 0.256 |
| 4Z8L Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex Deposited 2015-04-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1057–1396（340 aa）
Fragment：UNP residues 1057-1396
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2
|
Resolution 2.60 Å R-free 0.228 |
| 4Z8L Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex Deposited 2015-04-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1057–1396（340 aa）
Fragment：UNP residues 1057-1396
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2
|
Resolution 2.60 Å R-free 0.228 |
| 5AJA Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to Vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396) Deposited 2015-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1058–1396（339 aa）
Fragment：WD40-REPEAT DOMAIN, RESIDUES 1058-1396
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.16 M TRISODIUM CITRATE-HCL PH 5.2, 4% PEG 6000
|
Resolution 2.65 Å R-free 0.227 |
| 5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26 | Different construct 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
1045–1396（352 aa）
Fragment：UNP residues 1045-1396
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000
|
Resolution 3.49 Å R-free 0.206 |
| 5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26 | Different construct 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 E
1045–1396（352 aa）
Fragment：UNP residues 1045-1396
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000
|
Resolution 3.49 Å R-free 0.206 |
| 6N45 Crystal structure of the cryptic polo box domain of human activated Plk4 variant 1 Deposited 2018-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1475–1507（33 aa）
Chain B
1475–1507（33 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；4.3M Ammonium Acetate
0.1M BisTris propane
pH 8.0
|
Resolution 2.64 Å R-free 0.314 |
| 6ZUE Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1046–1396（351 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；100 mM Tri-Na citrate pH 5.5
18% PEG 1000
|
Resolution 3.09 Å R-free 0.279 |
| 6ZX9 Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1046–1396（351 aa）
|
Not recorded | GOL GLYCEROL × 8 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2.
|
Resolution 2.52 Å R-free 0.260 |
| 7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18 | 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 × 16 PDB declaration: Hexadecameric |
Chain B
2–1507（1506 aa）
Chain F
2–1507（1506 aa）
Chain J
2–1507（1506 aa）
Chain N
2–1507（1506 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.40 Å |
| 7SSE Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70 Deposited 2021-11-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1077–1390（314 aa）
Chain B
1077–1390（314 aa）
|
Mutation：F1077A, R1079A Mutation：F1077A, R1079A | B1I N-[(3R)-1-(3-fluorophenyl)piperidin-3-yl]-6-(morpholin-4-yl)pyrimidin-4-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；30% PEG3350 ,0.1M Ammonium Sulphate, 0.1M Bis-Tris pH5.5
|
Resolution 1.62 Å R-free 0.234 |
| 7UFV Crystal structure of the WDR domain of human DCAF1 in complex with OICR-6766 Deposited 2022-03-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1077–1390（314 aa）
|
Mutation：F1077A, R1079A | N6O (3P)-N-[(1S)-3-amino-1-(3-chlorophenyl)-3-oxopropyl]-3-(2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；20% PEG3350, 0.2M Potassium Fluoride
|
Resolution 1.90 Å R-free 0.254 |
| 7UFV Crystal structure of the WDR domain of human DCAF1 in complex with OICR-6766 Deposited 2022-03-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1077–1390（314 aa）
|
Mutation：F1077A, R1079A | N6O (3P)-N-[(1S)-3-amino-1-(3-chlorophenyl)-3-oxopropyl]-3-(2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 UNX UNKNOWN LIGAND × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；20% PEG3350, 0.2M Potassium Fluoride
|
Resolution 1.90 Å R-free 0.254 |
| 7V7B CryoEM structure of DDB1-VprBP complex in ARM-up conformation Deposited 2021-08-21 | 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 × 4 PDB declaration: tetrameric |
Chain A
1–1507（1507 aa）
Chain C
1–1507（1507 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7V7C CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex Deposited 2021-08-21 | 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 A
1–1507（1507 aa）
Chain E
1–1507（1507 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8F8E Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound Deposited 2022-11-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1077–1390（314 aa）
|
Mutation：F1077A, R1079A | XJI (3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M di-Ammonium Citrate
|
Resolution 1.55 Å R-free 0.209 |
| 8F8E Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound Deposited 2022-11-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1077–1390（314 aa）
|
Mutation：F1077A, R1079A | XJI (3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M di-Ammonium Citrate
|
Resolution 1.55 Å R-free 0.209 |
| 8OG5 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1 Deposited 2023-03-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1039–1401（363 aa）
|
Mutation：Q1250L | EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 LQH 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate
|
Resolution 2.20 Å R-free 0.235 |
| 8OG6 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1 Deposited 2023-03-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1039–1401（363 aa）
|
Mutation：Q1250L | LQH 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris pH 7.0, 2.13M Lithium acetate
|
Resolution 2.25 Å R-free 0.231 |
| 8OG7 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 2 Deposited 2023-03-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1039–1401（363 aa）
|
Mutation：Q1250L | ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 VMR (4~{R})-4-[3-(4-chloranylphenoxy)phenyl]pyrrolidin-2-imine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate
|
Resolution 2.64 Å R-free 0.206 |
| 8OG8 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 3 Deposited 2023-03-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1039–1401（363 aa）
|
Mutation：Q1250L | VM8 5-(2-methyl-1-phenyl-propan-2-yl)imidazo[2,1-a]isoquinoline × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate
|
Resolution 2.11 Å R-free 0.212 |
| 8OG9 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 4 Deposited 2023-03-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1039–1401（363 aa）
|
Mutation：Q1250L | VM3 5-[1-(4-chlorophenyl)cyclopropyl]imidazo[2,1-a]isoquinoline × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate
|
Resolution 2.94 Å R-free 0.240 |
| 8OGA Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 6 Deposited 2023-03-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain P
1079–1393（315 aa）
|
Mutation：Q1250L | EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 2 VLW 5-[1-(4-methoxyphenyl)cyclopropyl]-8-(4-methylpiperazin-1-yl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 1.66M Lithium acetate
|
Resolution 2.20 Å R-free 0.209 |
| 8OGB Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 8 Deposited 2023-03-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1039–1401（363 aa）
|
Mutation：Q1250L | EDO 1,2-ETHANEDIOL × 1 VN5 ~{N}'-[2-[1-(4-methoxyphenyl)cyclopropyl]-7-(4-methylpiperazin-1-yl)quinazolin-4-yl]ethane-1,2-diamine × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 2.13M Lithium acetate
|
Resolution 2.27 Å R-free 0.212 |
| 8OGC Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 11 Deposited 2023-03-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1039–1401（363 aa）
|
Mutation：Q1250L | DMS DIMETHYL SULFOXIDE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 1 VMZ 1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]ethanone × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 2.18M Lithium acetate
|
Resolution 2.09 Å R-free 0.202 |
| 8OO5 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 13 Deposited 2023-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain P
1079–1393（315 aa）
|
Mutation：Q1250L | VUF 1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclohexyl]quinazolin-7-yl]piperazin-1-yl]ethanone × 2 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.91M LiSO4, 0.1M Tris pH 7.5
|
Resolution 2.25 Å R-free 0.220 |
| 8OOD Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15 Deposited 2023-04-05 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1039–1401（363 aa）
|
Mutation：Q1250L | MG MAGNESIUM ION × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 5 VY3 ~{N}-[2-[2-[2-[2-[2-[2-[3-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]ethanamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.13M LiSO4, 0.1M Tris pH 7.5
|
Resolution 1.50 Å R-free 0.186 |
| 9B9H Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40333 Deposited 2024-04-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1080–1390（311 aa）
Fragment：residues 1080-1390
|
Not recorded | A1AM2 N-{(1P)-5'-({(17E)-18-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-16-oxo-3,6,9,12-tetraoxa-15-azaoctadec-17-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；5% w/v 1-ethyl-3-methylimidazolium ethyl sulfate, 15% w/v polyethylene glycol 20,000, pH 7.9
|
Resolution 2.06 Å R-free 0.229 |
| 9B9T Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40407 Deposited 2024-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1080–1390（311 aa）
Fragment：residues 1080-1390
|
Not recorded | A1ANM N-{(1P)-5'-[(17-{(4P)-4-[(2P)-4-{[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-1H-pyrazol-1-yl}-16-oxo-3,6,9,12-tetraoxa-15-azaheptadecan-1-yl)carbamoyl]-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate trihydrate, pH 4.6, 2.0 M sodium formate
|
Resolution 2.05 Å R-free 0.196 |
| 9B9W Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40792 Deposited 2024-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1080–1390（311 aa）
Fragment：residues 1080-1390
|
Not recorded | A1ANN (4P)-N-[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(25E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,24-dioxo-5,8,11,14,17,20-hexaoxa-2,23-diazahexacos-25-en-26-yl]-1H-pyrrole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；35% v/v tacsimate, pH 7.0
|
Resolution 1.92 Å R-free 0.183 |
| 9BA2 Crystal structure of the binary complex of DCAF1 and WDR5 Deposited 2024-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1080–1390（311 aa）
Fragment：residues 1080-1390
|
Not recorded | IMD IMIDAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M imidazole, pH 7.4, 20% w/v polyethylene glycol 4,000
|
Resolution 2.97 Å R-free 0.266 |
| 9BHR Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound Deposited 2024-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1077–1390（314 aa）
|
Not recorded | A1API (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(2-methoxyethyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate
|
Resolution 1.62 Å R-free 0.187 |
| 9BHR Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound Deposited 2024-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1077–1390（314 aa）
|
Not recorded | A1API (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(2-methoxyethyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate
|
Resolution 1.62 Å R-free 0.187 |
| 9BHS Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound Deposited 2024-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1077–1390（314 aa）
|
Not recorded | A1APJ (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrole-3-carboxamide × 1 UNL UNKNOWN LIGAND × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide
|
Resolution 1.43 Å R-free 0.170 |
| 9BHS Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound Deposited 2024-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1077–1390（314 aa）
|
Not recorded | A1APJ (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrole-3-carboxamide × 1 UNL UNKNOWN LIGAND × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide
|
Resolution 1.43 Å R-free 0.170 |
| 9C1Q Crystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 compound Deposited 2024-05-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1077–1390（314 aa）
|
Not recorded | A1ATT (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(3-methoxyprop-1-yn-1-yl)-1H-pyrrole-3-carboxamide × 1 UNX UNKNOWN LIGAND × 4 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate
|
Resolution 1.80 Å R-free 0.191 |
| 9D4E Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103 Deposited 2024-08-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1077–1390（314 aa）
|
Not recorded | A1A1Q (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M di-Ammonium Citrate
|
Resolution 1.70 Å R-free 0.206 |
| 9D4E Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103 Deposited 2024-08-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1077–1390（314 aa）
|
Not recorded | A1A1Q (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M di-Ammonium Citrate
|
Resolution 1.70 Å R-free 0.206 |
| 9DLW Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41114 Deposited 2024-09-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1080–1390（311 aa）
Fragment：residues 1080-1390
|
Not recorded | A1BAF N-{(1P)-5'-({(32E)-33-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-31-oxo-3,6,9,12,15,18,21,24,27-nonaoxa-30-azatritriacont-32-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.9；294 K；1.8 M Sodium phosphate monobasic monohydrate, potassium phosphate dibasic / pH 6.9
|
Resolution 2.07 Å R-free 0.242 |
| 9NSN Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41059 Deposited 2025-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1080–1390（311 aa）
Fragment：residues 1080-1390
|
Not recorded | A1B0X N-{(1P)-5'-({(26E)-27-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-25-oxo-3,6,9,12,15,18,21-heptaoxa-24-azaheptacos-26-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.15 M cesium chloride, 15% PEG3350
|
Resolution 1.85 Å R-free 0.234 |
| 9NSO Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41060 Deposited 2025-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1080–1390（311 aa）
Fragment：residues 1080-1390
|
Not recorded | A1B0Y (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(34E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,33-dioxo-5,8,11,14,17,20,23,26,29-nonaoxa-2,32-diazapentatriacont-34-en-35-yl]-1H-pyrrole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M sodium citrate tribasic dihydrate, pH 4.2, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic monohydrate
|
Resolution 1.85 Å R-free 0.218 |
| 9PLY Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156 Deposited 2025-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1077–1390（314 aa）
Chain B
1077–1390（314 aa）
|
Not recorded | A1CI0 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(3-methoxypropyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 2 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M Magnesium formate
|
Resolution 1.40 Å R-free 0.174 |
| 9Y4Q Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102 Deposited 2025-09-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1077–1390（314 aa）
Chain B
1077–1390（314 aa）
|
Not recorded | A1CR9 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(pyrimidin-5-yl)-1H-pyrrole-3-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；3.2 M NaCl, 0.1 M Bis-Tris Propane pH 7.0
|
Resolution 1.48 Å R-free 0.193 |
| 9Y76 Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120 Deposited 2025-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1077–1390（314 aa）
|
Not recorded | A1CSX (4P,5M)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{1-[2-(morpholin-4-yl)ethyl]-1H-pyrazol-4-yl}-1H-pyrrole-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M magnesium formate
|
Resolution 1.56 Å R-free 0.208 |
| 9Y76 Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120 Deposited 2025-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1077–1390（314 aa）
|
Not recorded | A1CSX (4P,5M)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{1-[2-(morpholin-4-yl)ethyl]-1H-pyrazol-4-yl}-1H-pyrrole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M magnesium formate
|
Resolution 1.56 Å R-free 0.208 |
| 9YDG Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074 Deposited 2025-09-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1080–1390（311 aa）
|
Not recorded | A1CU7 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-(morpholin-4-yl)-3-oxoprop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M Potassium Fluoride
|
Resolution 1.54 Å R-free 0.218 |
| 9YDG Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074 Deposited 2025-09-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1080–1390（311 aa）
|
Not recorded | A1CU7 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-(morpholin-4-yl)-3-oxoprop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M Potassium Fluoride
|
Resolution 1.54 Å R-free 0.218 |
| 9YE4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110 Deposited 2025-09-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1080–1390（311 aa）
|
Not recorded | A1CVQ (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% w/v PEG 3350, 0.1 M Ammonium Sulphate, 0.1 M Bis-Tris pH 5.5
|
Resolution 1.74 Å R-free 0.224 |
| 9YE4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110 Deposited 2025-09-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1080–1390（311 aa）
|
Not recorded | A1CVQ (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% w/v PEG 3350, 0.1 M Ammonium Sulphate, 0.1 M Bis-Tris pH 5.5
|
Resolution 1.74 Å R-free 0.224 |
| 9YV4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109 Deposited 2025-10-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1080–1390（311 aa）
|
Not recorded | A1CY9 (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(pyrrolidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 1 UNX UNKNOWN LIGAND × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% w/v PEG 3350, 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5
|
Resolution 1.60 Å R-free 0.194 |
| 9YV4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109 Deposited 2025-10-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1080–1390（311 aa）
|
Not recorded | A1CY9 (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(pyrrolidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% w/v PEG 3350, 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5
|
Resolution 1.60 Å R-free 0.194 |
| 9ZL9 Crystal structure of DCAF1 in complex with SDIPTAC C7 Deposited 2025-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1077–1390（314 aa）
Chain B
1077–1390（314 aa）
Chain C
1077–1390（314 aa）
Chain D
1077–1390（314 aa）
Chain E
1077–1390（314 aa）
Chain F
1077–1390（314 aa）
|
Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A | A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C23 (4P,4'P)-5,5'-[(1E,30E)-3,29-dioxo-7,10,13,16,19,22,25-heptaoxa-4,28-diazahentriaconta-1,30-diene-1,31-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.3；294.15 K；0.2 M sodium fluoride, 20% w/v PEG 3350, pH 7.3
|
Resolution 2.60 Å R-free 0.317 |
| 9ZLE Crystal structure of DCAF1 in complex with SDIPTAC C8 Deposited 2025-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1077–1390（314 aa）
Chain B
1077–1390（314 aa）
Chain C
1077–1390（314 aa）
Chain D
1077–1390（314 aa）
Chain E
1077–1390（314 aa）
Chain F
1077–1390（314 aa）
|
Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A | A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C25 (4P,4'P)-5,5'-[(1E,33E)-3,32-dioxo-7,10,13,16,19,22,25,28-octaoxa-4,31-diazatetratriaconta-1,33-diene-1,34-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；294.15 K；1.0 M ammonium tartrate dibasic, 0.1 M sodium acetate trihydrate, pH 4.6
|
Resolution 2.55 Å R-free 0.305 |
| 9ZLG Crystal structure of DCAF1 in complex with SDIPTAC C9 Deposited 2025-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
1077–1390（314 aa）
Chain B
1077–1390（314 aa）
Chain C
1077–1390（314 aa）
Chain D
1077–1390（314 aa）
Chain E
1077–1390（314 aa）
Chain F
1077–1390（314 aa）
Chain G
1077–1390（314 aa）
Chain H
1077–1390（314 aa）
|
Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A | A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C26 (4P,4'P)-5,5'-[(1E,36E)-3,35-dioxo-7,10,13,16,19,22,25,28,31-nonaoxa-4,34-diazaheptatriaconta-1,36-diene-1,37-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；5% w/v 1-ethyl-3-methylimidazolium acetate, 15% w/v PEG 20,000, pH 6.5
|
Resolution 2.30 Å R-free 0.289 |
| 9ZLI Crystal structure of DCAF1 in complex with SDIPTAC C11 Deposited 2025-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1077–1390（314 aa）
Chain B
1077–1390（314 aa）
Chain C
1077–1390（314 aa）
Chain D
1077–1390（314 aa）
Chain E
1077–1390（314 aa）
Chain F
1077–1390（314 aa）
|
Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.07 Å R-free 0.278 |
46 other PDB entries and 59 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | VPRBP_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 19–381； UniProt 1039–1401 Author chain B； PDBConstruct 19–381； UniProt 1039–1401 |