Structure of PDB 5nge Chain A Binding Site BS01

Receptor Information
>5nge 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]
GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQ
RVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKM
KGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIF
ESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMY
DPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNH
GGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHCTNAYMLVYI
RESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQKRK
Ligand information
Ligand ID8WK
InChIInChI=1S/C24H23F4N7O3/c25-15-1-3-16(4-2-15)35-22-17(12-30-35)23(37)33(14-29-22)13-24(38)6-9-32(10-7-24)20(36)11-18(21(27)28)34-8-5-19(26)31-34/h1-5,8,12,14,18,21,38H,6-7,9-11,13H2/t18-/m0/s1
InChIKeyBLSNYSFLZAWBIV-SFHVURJKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(ccc1n2c3c(cn2)C(=O)N(C=N3)CC4(CCN(CC4)C(=O)C[C@@H](C(F)F)n5ccc(n5)F)O)F
CACTVS 3.385OC1(CCN(CC1)C(=O)C[C@@H](C(F)F)n2ccc(F)n2)CN3C=Nc4n(ncc4C3=O)c5ccc(F)cc5
OpenEye OEToolkits 2.0.6c1cc(ccc1n2c3c(cn2)C(=O)N(C=N3)CC4(CCN(CC4)C(=O)CC(C(F)F)n5ccc(n5)F)O)F
CACTVS 3.385OC1(CCN(CC1)C(=O)C[CH](C(F)F)n2ccc(F)n2)CN3C=Nc4n(ncc4C3=O)c5ccc(F)cc5
FormulaC24 H23 F4 N7 O3
Name5-[[1-[(3~{S})-4,4-bis(fluoranyl)-3-(3-fluoranylpyrazol-1-yl)butanoyl]-4-oxidanyl-piperidin-4-yl]methyl]-1-(4-fluorophenyl)pyrazolo[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL4759513
DrugBank
ZINC
PDB chain5nge 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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PDB5nge Molecular basis of USP7 inhibition by selective small-molecule inhibitors.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		Y224 D295 Q297 Q351 L406 M407 R408 F409 H456 D459 N460 H461 Y465 Y514
Binding residue
(residue number reindexed from 1)		Y13 D84 Q86 Q140 L195 M196 R197 F198 H245 D248 N249 H250 Y254 Y295
Annotation score1
Binding affinityMOAD: Kd=65nM
PDBbind-CN: -logKd/Ki=7.19,Kd=65nM
Enzymatic activity
Catalytic site (original residue number in PDB) N218 C223 H464 D481
Catalytic site (residue number reindexed from 1) N7 C12 H253 D270
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:5nge, PDBe:5nge, PDBj:5nge
PDBsum5nge
PubMed29045389
UniProtQ93009|UBP7_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (Gene Name=USP7)

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