Structure of PDB 5ngf Chain A Binding Site BS01

Receptor Information
>5ngf Chain A (length=332) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPL
ALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVE
NKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKK
NIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMR
FMYNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGH
YVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHCTNAYMLVYIRES
KLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK
Ligand information
Ligand ID8WN
InChIInChI=1S/C27H30N6O5S/c1-3-39(37,38)30-23-7-5-4-6-21(23)19-8-10-20(11-9-19)25(34)32-14-12-27(36,13-15-32)17-33-18-28-24-22(26(33)35)16-29-31(24)2/h4-11,16,18,30,36H,3,12-15,17H2,1-2H3
InChIKeyRLNXXNBZMTXHGJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC[S](=O)(=O)Nc1ccccc1c2ccc(cc2)C(=O)N3CCC(O)(CC3)CN4C=Nc5n(C)ncc5C4=O
OpenEye OEToolkits 2.0.6CCS(=O)(=O)Nc1ccccc1c2ccc(cc2)C(=O)N3CCC(CC3)(CN4C=Nc5c(cnn5C)C4=O)O
FormulaC27 H30 N6 O5 S
Name~{N}-[2-[4-[4-[(1-methyl-4-oxidanylidene-pyrazolo[3,4-d]pyrimidin-5-yl)methyl]-4-oxidanyl-piperidin-1-yl]carbonylphenyl]phenyl]ethanesulfonamide
ChEMBL
DrugBank
ZINC
PDB chain5ngf 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

[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]
PDB5ngf Molecular basis of USP7 inhibition by selective small-molecule inhibitors.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		C223 Y224 M292 D295 Q297 M407 F409 Y465
Binding residue
(residue number reindexed from 1)		C15 Y16 M84 D87 Q89 M199 F201 Y251
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.11,Kd=7.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) N218 C223 H464 D481
Catalytic site (residue number reindexed from 1) N10 C15 H250 D267
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:5ngf, PDBe:5ngf, PDBj:5ngf
PDBsum5ngf
PubMed29045389
UniProtQ93009|UBP7_HUMAN Ubiquitin carboxyl-terminal hydrolase 7 (Gene Name=USP7)

[Back to BioLiP]