Structure of PDB 5vs6 Chain A Binding Site BS01

Receptor Information
>5vs6 Chain A (length=339) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVP
LALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNV
ENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGK
KNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLM
RFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHS
GDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHCTNAYM
LVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK
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 A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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 M407 F409 K420 H456 N460 H461 Y465 Y514
Binding residue
(residue number reindexed from 1)		Y17 D88 Q90 M200 F202 K213 H249 N253 H254 Y258 Y299
Annotation score1
Binding affinityMOAD: Kd=104nM
PDBbind-CN: -logKd/Ki=6.98,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) N11 C16 H257 D274
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
View graph for
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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