Structure of PDB 6vn2 Chain B Binding Site BS01

Receptor Information
>6vn2 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]
SKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSV
PLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDN
VENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKG
KKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQL
MRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVH
SGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGCTNAYML
VYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQ
Ligand information
Ligand IDR44
InChIInChI=1S/C25H23ClN4O4S/c26-15-9-14-10-20(25(33)29-7-5-27-6-8-29)34-23(14)18(11-15)17-3-4-28-19-12-16(35-24(17)19)13-30-21(31)1-2-22(30)32/h3-4,9,11-12,20,27H,1-2,5-8,10,13H2/t20-/m1/s1
InChIKeyHDYYKIHPDVFOOZ-HXUWFJFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Clc1cc2C[C@@H](Oc2c(c1)c3ccnc4cc(CN5C(=O)CCC5=O)sc34)C(=O)N6CCNCC6
CACTVS 3.385Clc1cc2C[CH](Oc2c(c1)c3ccnc4cc(CN5C(=O)CCC5=O)sc34)C(=O)N6CCNCC6
OpenEye OEToolkits 2.0.7c1cnc2cc(sc2c1c3cc(cc4c3OC(C4)C(=O)N5CCNCC5)Cl)CN6C(=O)CCC6=O
OpenEye OEToolkits 2.0.7c1cnc2cc(sc2c1c3cc(cc4c3O[C@H](C4)C(=O)N5CCNCC5)Cl)CN6C(=O)CCC6=O
ACDLabs 12.01c1(Cl)cc(c2c(c1)CC(O2)C(N3CCNCC3)=O)c5ccnc6cc(CN4C(=O)CCC4=O)sc56
FormulaC25 H23 Cl N4 O4 S
Name1-({7-[(2R)-5-chloro-2-(piperazine-1-carbonyl)-2,3-dihydro-1-benzofuran-7-yl]thieno[3,2-b]pyridin-2-yl}methyl)-1H-pyrrole-2,5-dione
ChEMBLCHEMBL4640002
DrugBank
ZINC
PDB chain6vn2 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]
PDB6vn2 Discovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with In Vivo Antitumor Activity.
Resolution2.93 Å
Binding residue
(original residue number in PDB)		M292 H294 D295 V296 M407 R408 F409 H456 N460 Y465 Y514
Binding residue
(residue number reindexed from 1)		M86 H88 D89 V90 M201 R202 F203 H250 N254 Y259 Y298
Annotation score1
Binding affinityBindingDB: IC50=0.180000nM
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:6vn2, PDBe:6vn2, PDBj:6vn2
PDBsum6vn2
PubMed32302140
UniProtQ93009|UBP7_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (Gene Name=USP7)

[Back to BioLiP]