Structure of PDB 5n9t Chain A Binding Site BS01

Receptor Information
>5n9t Chain A (length=357) 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
SGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLS
VRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQKRK
ERQEHHH
Ligand information
Ligand ID8QQ
InChIInChI=1S/C29H31F3N6O3/c1-36-26(21-9-7-19(16-33)8-10-21)24-25(35-36)27(40)38(18-34-24)17-28(41)11-13-37(14-12-28)23(39)15-22(29(30,31)32)20-5-3-2-4-6-20/h2-10,18,22,41H,11-17,33H2,1H3/t22-/m1/s1
InChIKeyRLPQYKGBXQQARM-JOCHJYFZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1nc2C(=O)N(CC3(O)CCN(CC3)C(=O)C[C@H](c4ccccc4)C(F)(F)F)C=Nc2c1c5ccc(CN)cc5
CACTVS 3.385Cn1nc2C(=O)N(CC3(O)CCN(CC3)C(=O)C[CH](c4ccccc4)C(F)(F)F)C=Nc2c1c5ccc(CN)cc5
OpenEye OEToolkits 2.0.6Cn1c(c2c(n1)C(=O)N(C=N2)CC3(CCN(CC3)C(=O)CC(c4ccccc4)C(F)(F)F)O)c5ccc(cc5)CN
OpenEye OEToolkits 2.0.6Cn1c(c2c(n1)C(=O)N(C=N2)CC3(CCN(CC3)C(=O)C[C@H](c4ccccc4)C(F)(F)F)O)c5ccc(cc5)CN
FormulaC29 H31 F3 N6 O3
Name3-[4-(aminomethyl)phenyl]-2-methyl-6-[[4-oxidanyl-1-[(3~{R})-4,4,4-tris(fluoranyl)-3-phenyl-butanoyl]piperidin-4-yl]methyl]pyrazolo[4,3-d]pyrimidin-7-one
ChEMBLCHEMBL4283787
DrugBank
ZINC
PDB chain5n9t Chain A Residue 1005 [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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PDB5n9t Discovery and characterization of highly potent and selective allosteric USP7 inhibitors.
Resolution1.73 Å
Binding residue
(original residue number in PDB)		Y224 D295 Q297 Q351 L406 M407 R408 F409 K420 H456 N460 H461 Y465 Y514
Binding residue
(residue number reindexed from 1)		Y18 D89 Q91 Q145 L200 M201 R202 F203 K214 H250 N254 H255 Y259 Y308
Annotation score1
Binding affinityMOAD: ic50=22nM
PDBbind-CN: -logKd/Ki=6.66,IC50=220nM
BindingDB: IC50=22nM
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:5n9t, PDBe:5n9t, PDBj:5n9t
PDBsum5n9t
PubMed29200206
UniProtQ93009|UBP7_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (Gene Name=USP7)

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