8vw5

Crystal structure of Cbl-b TKB bound to compound 2

Method: X-RAY DIFFRACTION D_max: 82.8 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase CBL-B

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 36–343	Fragment：Cbl-PTB domain, residues 36-343	MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 A1AD4 [5-(2-{(2R,5S)-2-[2-(carboxymethoxy)-3-methoxy-5-nitrophenyl]-3,5-dimethyl-4-oxoimidazolidin-1-yl}-2-oxoethyl)-3,6-dimethoxy-9,9-dimethyl-9H-xanthen-4-yl]acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ca(OAc)2, 0.1 M NaCacodylate pH 6.5, 18% PEG8000	Resolution 1.76 Å R-free 0.204
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 36–343	Fragment：Cbl-PTB domain, residues 36-343	CA CALCIUM ION × 1 A1AD4 [5-(2-{(2R,5S)-2-[2-(carboxymethoxy)-3-methoxy-5-nitrophenyl]-3,5-dimethyl-4-oxoimidazolidin-1-yl}-2-oxoethyl)-3,6-dimethoxy-9,9-dimethyl-9H-xanthen-4-yl]acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ca(OAc)2, 0.1 M NaCacodylate pH 6.5, 18% PEG8000	Resolution 1.76 Å R-free 0.204

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 8VW5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AK5 beta PIX-SH3 complexed with a Cbl-b peptide Deposited 2005-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 904–911（8 aa） Fragment：residues 904-911	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；291 K；PEG 3000, SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 6.50	Resolution 1.85 Å R-free 0.269
2BZ8 N-terminal Sh3 domain of CIN85 bound to Cbl-b peptide Deposited 2005-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 902–912（11 aa） Fragment：POLYPROLINE RICH REGION RESIDUES 902-912	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.8 M NA CITRATE, 0.1 M BIS-TRIS PH 7.5, 0.2 M NACL	Resolution 2.00 Å R-free 0.271
2DO6 Solution structure of RSGI RUH-065, a UBA domain from human cDNA Deposited 2006-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 931–970（40 aa） Fragment：UBA domain Chain B 931–970（40 aa） Fragment：UBA domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure AMBIENT NMR sample composition 1.1mM UBA domain U-15N,13C, 20mM d-Tris-HCl buffer (pH 7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0mM UBA domain U-15N,13C, 1.0mM UBA domain, 20mM d-Tris-HCl buffer (pH 7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 100% D2O \| 100% D2O	Resolution not provided
2J6F N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) BOUND TO CBL-B PEPTIDE Deposited 2006-09-28	Different construct 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 902–912（11 aa） Fragment：PEPTIDE, RESIDUES 902-912	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；20% PEG3000, 0.1M ACETATE PH 5.5	Resolution 1.70 Å R-free 0.218
2JNH Solution Structure of the UBA Domain from Cbl-b Deposited 2007-01-24	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 926–971（46 aa） Fragment：UBA domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 1 mM [U-13C; U-15N] entity, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.01 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LDR Solution structure of Helix-RING domain of Cbl-b in the Tyr363 phosphorylated form Deposited 2011-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 351–426（76 aa） Fragment：Helix-RING domain, residues 345-426	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 20mM MES-1, 2mM DTT-2, 150mM sodium chloride-3, 0.4mM [U-99% 13C; U-99% 15N] protein-4, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2OOA crystal structure of the UBA domain from Cbl-b ubiquitin ligase Deposited 2007-01-25	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 924–973（50 aa） Fragment：UBA domain	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；pH 8.2；293 K；1.2M sodium/potassium phosphate, 12% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.56 Å R-free 0.240
2OOA crystal structure of the UBA domain from Cbl-b ubiquitin ligase Deposited 2007-01-25	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 924–973（50 aa） Fragment：UBA domain	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；pH 8.2；293 K；1.2M sodium/potassium phosphate, 12% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.56 Å R-free 0.240
2OOB crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin Deposited 2007-01-25	Different construct 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 924–973（50 aa） Fragment：UBA domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.2M calcium chloride, 0.1M sodium acetate, 20% PEG6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.256
3PFV Crystal structure of Cbl-b TKB domain in complex with EGFR pY1069 peptide Deposited 2010-10-29	Different construct 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 38–344（307 aa） Fragment：N-terminal TKB domain (UNP residues 38-344)	Not recorded	NA SODIUM ION × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；30% PEG 3350, 0.3M Ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.27 Å R-free 0.262
3PFV Crystal structure of Cbl-b TKB domain in complex with EGFR pY1069 peptide Deposited 2010-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 38–344（307 aa） Fragment：N-terminal TKB domain (UNP residues 38-344)	Not recorded	NA SODIUM ION × 1 SO4 SULFATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；30% PEG 3350, 0.3M Ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.27 Å R-free 0.262
3VGO Crystal structure of the N-terminal fragment of Cbl-b Deposited 2011-08-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 39–426（388 aa） Fragment：N-terminal fragment, UNP residues 39-426	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；25% PEG 3350, 0.1M bicine, 0.8M KNO3, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.10 Å R-free 0.328
3VGO Crystal structure of the N-terminal fragment of Cbl-b Deposited 2011-08-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 39–426（388 aa） Fragment：N-terminal fragment, UNP residues 39-426	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；25% PEG 3350, 0.1M bicine, 0.8M KNO3, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.10 Å R-free 0.328
3VGO Crystal structure of the N-terminal fragment of Cbl-b Deposited 2011-08-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 39–426（388 aa） Fragment：N-terminal fragment, UNP residues 39-426	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；25% PEG 3350, 0.1M bicine, 0.8M KNO3, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.10 Å R-free 0.328
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14	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 A 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE	Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14	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 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE	Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14	Different construct Different mutation/modification 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 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE	Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14	Different construct 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 M 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE	Resolution 2.21 Å R-free 0.211
8GCY Co-crystal structure of CBL-B in complex with N-Aryl isoindolin-1-one inhibitor Deposited 2023-03-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–427（390 aa）	Not recorded	ZN ZINC ION × 2 Z3N 2-{3-[(1s,3R)-3-methyl-1-(4-methyl-4H-1,2,4-triazol-3-yl)cyclobutyl]phenyl}-6-{[(3S)-3-methylpiperidin-1-yl]methyl}-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M Imidazole, 0.1 M MES monohydrate pH 6.5 0.09 M Sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09M Ammonium sulfate 12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350	Resolution 1.81 Å R-free 0.230
8QNG Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (benzodiazepine HTS hit compound 1) Deposited 2023-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	W89 2-(morpholin-4-ylmethyl)-~{N}-[(3~{S})-2-oxidanylidene-5-phenyl-1,3-dihydro-1,4-benzodiazepin-3-yl]benzamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；9 % PEG8000, 0.05 M MgAcetate, 0.05 M PCTP pH 7.5	Resolution 2.20 Å R-free 0.295
8QNH Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (WO2020264398 Ex23) Deposited 2023-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	Z3N 2-{3-[(1s,3R)-3-methyl-1-(4-methyl-4H-1,2,4-triazol-3-yl)cyclobutyl]phenyl}-6-{[(3S)-3-methylpiperidin-1-yl]methyl}-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；9 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8	Resolution 2.00 Å R-free 0.248
8QNI Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (benzodiazepine compound 25) Deposited 2023-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	W7R 2-[[(2~{S})-2-methylmorpholin-4-yl]methyl]-~{N}-[(3~{S})-2-oxidanylidene-5-phenyl-1,3-dihydropyrido[3,4-e][1,4]diazepin-3-yl]benzamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCPT pH 8.0	Resolution 2.48 Å R-free 0.286
8QTG Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 9) Deposited 2023-10-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	WUQ 3-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-5-(trifluoromethyl)-1~{H}-pyridin-2-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8-11 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8	Resolution 1.42 Å R-free 0.243
8QTH Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 8) Deposited 2023-10-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	WX0 1-methyl-5-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-3-(trifluoromethyl)-7H-pyrrolo[2,3-b]pyridin-6-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8-11 % PEG8000, 2.5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8	Resolution 2.20 Å R-free 0.260
8QTJ Crystal structure of Cbl-b in complex with an allosteric inhibitor (compound 30) Deposited 2023-10-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1 WUI 3-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-1-[(1~{R})-1-(1-methylpyrazol-4-yl)ethyl]-5-(trifluoromethyl)pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8-11 % PEG8000, 2.5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8	Resolution 1.52 Å R-free 0.232
8QTK Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 31) Deposited 2023-10-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1 WX9 3-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-1-[(1S)-1-(1-methylpyrazol-4-yl)ethyl]-5-(trifluoromethyl)pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8-11 % PEG8000, 2.5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8	Resolution 1.87 Å R-free 0.268
8VW4 Crystal structure of Cbl-b TKB bound to compound 26 Deposited 2024-01-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–343（308 aa） Fragment：Cbl-PTB domain, residues 36-343	Not recorded	MG MAGNESIUM ION × 1 A1AEG (7-methoxy-2-{2-[(1S,3S,4S)-3-(3-methoxy-2-methyl-5-nitrophenyl)-1-methyl-5-oxo-1,5-dihydroimidazo[1,5-a]pyridin-2(3H)-yl]-2-oxoethoxy}quinolin-8-yl)acetic acid × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M NaCitrate, 20% PEG3350	Resolution 2.40 Å R-free 0.253
8VW4 Crystal structure of Cbl-b TKB bound to compound 26 Deposited 2024-01-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–343（308 aa） Fragment：Cbl-PTB domain, residues 36-343	Not recorded	MG MAGNESIUM ION × 1 A1AEG (7-methoxy-2-{2-[(1S,3S,4S)-3-(3-methoxy-2-methyl-5-nitrophenyl)-1-methyl-5-oxo-1,5-dihydroimidazo[1,5-a]pyridin-2(3H)-yl]-2-oxoethoxy}quinolin-8-yl)acetic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M NaCitrate, 20% PEG3350	Resolution 2.40 Å R-free 0.253
9FQH E3 ligase Cbl-b in complex with a triazolone core inhibitor (compound 1) Deposited 2024-06-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	A1IEW 8-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-3-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-5-(trifluoromethyl)-1$l^{4},7,8-triazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；9 % PEG8000, 5 % MPD, 0.05 M MgAcetate, 0.05 M PCTP pH 8	Resolution 1.79 Å R-free 0.249
9FQI E3 ligase Cbl-b in complex with a lactam scaffold inhibitor (compound 7) Deposited 2024-06-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa）	Not recorded	A1IEV 8-[3-[(4~{R})-4-methyl-2-oxidanylidene-piperidin-4-yl]phenyl]-3-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-5-(trifluoromethyl)-1$l^{4},7,8-triazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG8000, 0.05 M Mg Acetate, 5 % MPD, 0.05 M PCPT pH 8.0	Resolution 1.95 Å R-free 0.291
9FQJ E3 ligase Cbl-b in complex with a carbamate scaffold inhibitor (compound 12) Deposited 2024-06-17	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 36–427（392 aa）	Mutation：EC:2.3.2.27	A1IE5 2-cyclopropyl-6-methyl-~{N}-[3-[(6~{S})-6-methyl-2-oxidanylidene-1,3-oxazinan-6-yl]phenyl]pyrimidine-4-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG8000, 0.05 M Mg Acetate, 5 % MPD, 0.05 M PCPT pH 8.0	Resolution 1.56 Å R-free 0.222
9FQJ E3 ligase Cbl-b in complex with a carbamate scaffold inhibitor (compound 12) Deposited 2024-06-17	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 36–427（392 aa）	Mutation：EC:2.3.2.27	A1IE5 2-cyclopropyl-6-methyl-~{N}-[3-[(6~{S})-6-methyl-2-oxidanylidene-1,3-oxazinan-6-yl]phenyl]pyrimidine-4-carboxamide × 1 ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；11 % PEG8000, 0.05 M Mg Acetate, 5 % MPD, 0.05 M PCPT pH 8.0	Resolution 1.56 Å R-free 0.222

23 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBLB_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 3–310； UniProt 36–343 Author chain B； PDBConstruct 3–310； UniProt 36–343

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8vw5
Deposition date deposition_date	2024-01-31
最后修订 last_revision	2024-07-03
Structure title title	Crystal structure of Cbl-b TKB bound to compound 2
Keywords keywords	Ubiquitin ligase, E3, inhibitor, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.25 Å
Radius of gyration Rg (electron density) rg_electron	27.04 Å
Forward intensity I(0) i0	80091700.00
Molecular weight molecular_weight	72370.0 kDa
Excluded volume excluded_volume	91535 Å³
Envelope volume envelope_volume	113160 Å³
Hydration-shell volume shell_volume	34372 Å³
Envelope diameter envelope_diameter	85.8 Å
Shell Rg shell_rg	34.99 Å
Envelope Rg envelope_rg	26.61 Å
Shape Rg shape_rg	27.03 Å
Total Rg total_rg	27.91 Å
Total atoms total_atoms	5186
Residues n_residues	608
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.8 Å
Rg (real space) rg_real	28.05 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	8.0090e+07
I(0) uncertainty (real space) i0_real_error	9.4620e+05
Rg (reciprocal space) rg_reciprocal	28.12 Å
I(0) (reciprocal space) i0_reciprocal	80100000.0000
Solution quality estimate total_estimate	0.9119
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.4 Å
Skewness Skewness skewness	0.100
Kurtosis Kurtosis kurtosis	-0.545
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18810000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.930

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase CBL-B
Molecular weight formula_weight	36205.5 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5820

GSPKQAAADRRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSRYDDNQKLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEENSQDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPDGRSYNPDLTG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	E3 ubiquitin-protein ligase CBL-B
Molecular weight formula_weight	36164.5 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSPKQAAADRRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYDDNQKLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEENSQDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDTFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPDGRSYNPDLTG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	;[5-(2-{(2R,5S)-2-[2-(carboxymethoxy)-3-methoxy-5-nitrophenyl]-3,5-dimethyl-4-oxoimidazolidin-1-yl}-2-oxoethyl)-3,6-dimethoxy-9,9-dimethyl-9H-xanthen-4-yl]acetic acid ;
Molecular weight formula_weight	707.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	616

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8. Citations (1)

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Unit-cell length a length_a	55.198 Å
Unit-cell length b length_b	56.820 Å
Unit-cell length c length_c	71.568 Å
Unit-cell angle α angle_alpha	102.90 °
Unit-cell angle β angle_beta	96.55 °
Unit-cell angle γ angle_gamma	111.97 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	35.880 Å
R factor r_factor	0.1767
R_work r_work	0.1753
R_free r_free	0.2041

fit	/app/data/saxs_computation/vw/8vw5/8vw5.fit
pddf	/app/data/pr_computation/vw/8vw5/8vw5.pr.out
profile	/app/data/saxs_computation/vw/8vw5/8vw5.dat

Crystal structure of Cbl-b TKB bound to compound 2

1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase CBL-B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)