Structure of PDB 6vn5 Chain A Binding Site BS01

Receptor Information
>6vn5 Chain A (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSV
PLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDN
VENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKG
KKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQL
MRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVH
SGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGTNAYML
VYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQ
Ligand information
Ligand IDR41
InChIInChI=1S/C18H19ClN4O2/c19-13-7-12-8-15(18(24)23-5-3-21-4-6-23)25-17(12)14(10-13)11-1-2-22-16(20)9-11/h1-2,7,9-10,15,21H,3-6,8H2,(H2,20,22)/t15-/m1/s1
InChIKeyJGHCITCCEQEXTL-OAHLLOKOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cnc(cc1c2cc(cc3c2OC(C3)C(=O)N4CCNCC4)Cl)N
OpenEye OEToolkits 2.0.7c1cnc(cc1c2cc(cc3c2O[C@H](C3)C(=O)N4CCNCC4)Cl)N
ACDLabs 12.01c1(cc(ccn1)c2cc(cc3c2OC(C3)C(=O)N4CCNCC4)Cl)N
CACTVS 3.385Nc1cc(ccn1)c2cc(Cl)cc3C[C@@H](Oc23)C(=O)N4CCNCC4
CACTVS 3.385Nc1cc(ccn1)c2cc(Cl)cc3C[CH](Oc23)C(=O)N4CCNCC4
FormulaC18 H19 Cl N4 O2
Name[(2R)-7-(2-aminopyridin-4-yl)-5-chloro-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone
ChEMBL
DrugBank
ZINC
PDB chain6vn5 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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PDB6vn5 Discovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with In Vivo Antitumor Activity.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		Y224 M292 H294 V296 F409 H456 Y465 Y514
Binding residue
(residue number reindexed from 1)		Y18 M86 H88 V90 F203 H250 Y259 Y298
Annotation score1
Binding affinityBindingDB: IC50=5600nM
Enzymatic activity
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vn5, PDBe:6vn5, PDBj:6vn5
PDBsum6vn5
PubMed32302140
UniProtQ93009|UBP7_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (Gene Name=USP7)

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