Structure of PDB 5vs6 Chain B Binding Site BS01

Receptor Information
>5vs6 Chain B (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPL
ALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVE
NKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKK
NIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMR
FMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSG
DNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGCTNAYMLV
YIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK
Ligand information
Ligand ID9QD
InChIInChI=1S/C32H42N6O4/c1-24(25-6-4-3-5-7-25)20-30(40)37-14-11-32(42,12-15-37)22-38-23-33-28-21-26(8-9-27(28)31(38)41)34-29(39)10-13-36-18-16-35(2)17-19-36/h3-9,21,23-24,42H,10-20,22H2,1-2H3,(H,34,39)/t24-/m1/s1
InChIKeyQLBYDWATOPNXBG-XMMPIXPASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@H](CC(=O)N1CCC(CC1)(CN2C=Nc3cc(ccc3C2=O)NC(=O)CCN4CCN(CC4)C)O)c5ccccc5
ACDLabs 12.01N4(CCC(CN2C=Nc3cc(NC(=O)CCN1CCN(C)CC1)ccc3C2=O)(CC4)O)C(=O)CC(c5ccccc5)C
CACTVS 3.385C[CH](CC(=O)N1CCC(O)(CC1)CN2C=Nc3cc(NC(=O)CCN4CCN(C)CC4)ccc3C2=O)c5ccccc5
OpenEye OEToolkits 2.0.6CC(CC(=O)N1CCC(CC1)(CN2C=Nc3cc(ccc3C2=O)NC(=O)CCN4CCN(CC4)C)O)c5ccccc5
CACTVS 3.385C[C@H](CC(=O)N1CCC(O)(CC1)CN2C=Nc3cc(NC(=O)CCN4CCN(C)CC4)ccc3C2=O)c5ccccc5
FormulaC32 H42 N6 O4
NameN-[3-({4-hydroxy-1-[(3R)-3-phenylbutanoyl]piperidin-4-yl}methyl)-4-oxo-3,4-dihydroquinazolin-7-yl]-3-(4-methylpiperazin-1-yl)propanamide
ChEMBLCHEMBL4548694
DrugBank
ZINC
PDB chain5vs6 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vs6 Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7.
Resolution2.27 Å
Binding residue
(original residue number in PDB)		Y224 D295 Q297 L406 M407 R408 F409 K420 H456 N460 H461 Y465 Y514
Binding residue
(residue number reindexed from 1)		Y16 D87 Q89 L198 M199 R200 F201 K212 H248 N252 H253 Y257 Y297
Annotation score1
Binding affinityMOAD: Kd=104nM
BindingDB: IC50=90nM
Enzymatic activity
Catalytic site (original residue number in PDB) N218 C223 H464 D481
Catalytic site (residue number reindexed from 1) N10 C15 H256 D273
Enzyme Commision number 3.4.19.12: ubiquitinyl hydrolase 1.
Gene Ontology
Molecular Function
GO:0004843 cysteine-type deubiquitinase activity
Biological Process
GO:0016579 protein deubiquitination

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Molecular Function
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Biological Process
External links
PDB RCSB:5vs6, PDBe:5vs6, PDBj:5vs6
PDBsum5vs6
PubMed29056421
UniProtQ93009|UBP7_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (Gene Name=USP7)

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