Structure of PDB 6vn3 Chain B Binding Site BS01

Receptor Information
>6vn3 Chain B (length=338) 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
SGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGCTNAYM
LVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQ
Ligand information
Ligand IDR3Y
InChIInChI=1S/C23H21ClFN3O3S/c1-12-6-13(24)7-16(22(12)31-19-10-26-9-17(19)25)15-4-5-27-18-8-14(32-23(15)18)11-28-20(29)2-3-21(28)30/h4-8,17,19,26H,2-3,9-11H2,1H3/t17-,19+/m0/s1
InChIKeySWLBIOVQZDSJKD-PKOBYXMFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1cc(cc(c1OC2CNCC2F)c3ccnc4c3sc(c4)CN5C(=O)CCC5=O)Cl
CACTVS 3.385Cc1cc(Cl)cc(c1O[C@@H]2CNC[C@@H]2F)c3ccnc4cc(CN5C(=O)CCC5=O)sc34
ACDLabs 12.01Cc4cc(Cl)cc(c2ccnc3cc(CN1C(CCC1=O)=O)sc23)c4OC5CNCC5F
OpenEye OEToolkits 2.0.7Cc1cc(cc(c1O[C@@H]2CNC[C@@H]2F)c3ccnc4c3sc(c4)CN5C(=O)CCC5=O)Cl
CACTVS 3.385Cc1cc(Cl)cc(c1O[CH]2CNC[CH]2F)c3ccnc4cc(CN5C(=O)CCC5=O)sc34
FormulaC23 H21 Cl F N3 O3 S
Name1-{[7-(5-chloro-2-{[(3R,4S)-4-fluoropyrrolidin-3-yl]oxy}-3-methylphenyl)thieno[3,2-b]pyridin-2-yl]methyl}-1H-pyrrole-2,5-dione
ChEMBLCHEMBL4641569
DrugBank
ZINC
PDB chain6vn3 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6vn3 Discovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with In Vivo Antitumor Activity.
Resolution2.73 Å
Binding residue
(original residue number in PDB)		M292 H294 D295 V296 Q297 M407 R408 F409 H456 Y465 Y514
Binding residue
(residue number reindexed from 1)		M86 H88 D89 V90 Q91 M201 R202 F203 H250 Y259 Y299
Annotation score1
Binding affinityBindingDB: IC50=1.2nM,EC50=560nM
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:6vn3, PDBe:6vn3, PDBj:6vn3
PDBsum6vn3
PubMed32302140
UniProtQ93009|UBP7_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (Gene Name=USP7)

[Back to BioLiP]