Structure of PDB 5d7q Chain B Binding Site BS03

Receptor Information
>5d7q Chain B (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYD
NLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLL
KDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYP
LSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVD
LLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGG
GMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ
Ligand information
Ligand ID4I5
InChIInChI=1S/C14H15ClN2O/c15-8-5-6-12-11(7-8)9-3-1-2-4-10(14(16)18)13(9)17-12/h5-7,10,17H,1-4H2,(H2,16,18)/t10-/m0/s1
InChIKeyABIVOOWWGYJNLV-JTQLQIEISA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC(=O)[C@H]1CCCCc2c1[nH]c3ccc(Cl)cc23
OpenEye OEToolkits 1.7.6c1cc2c(cc1Cl)c3c([nH]2)C(CCCC3)C(=O)N
OpenEye OEToolkits 1.7.6c1cc2c(cc1Cl)c3c([nH]2)[C@H](CCCC3)C(=O)N
CACTVS 3.370NC(=O)[CH]1CCCCc2c1[nH]c3ccc(Cl)cc23
ACDLabs 12.01Clc2cc1c3c(nc1cc2)C(C(=O)N)CCCC3
FormulaC14 H15 Cl N2 O
Name(6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide
ChEMBLCHEMBL198609
DrugBank
ZINCZINC000000499303
PDB chain5d7q Chain B Residue 403 [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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PDB5d7q Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		P94 F96 Q167 N168 I169 D170 I232 F234
Binding residue
(residue number reindexed from 1)		P39 F41 Q112 N113 I114 D115 I177 F179
Annotation score1
Binding affinityMOAD: ic50=2.8uM
BindingDB: IC50=2770nM
Enzymatic activity
Catalytic site (original residue number in PDB) P94 D95 F96 R97 N168 D170 H187
Catalytic site (residue number reindexed from 1) P39 D40 F41 R42 N113 D115 H132
Enzyme Commision number 2.3.1.-
2.3.1.286: protein acetyllysine N-acetyltransferase.
Gene Ontology
Molecular Function
GO:0017136 NAD-dependent histone deacetylase activity
GO:0051287 NAD binding
GO:0070403 NAD+ binding

View graph for
Molecular Function
External links
PDB RCSB:5d7q, PDBe:5d7q, PDBj:5d7q
PDBsum5d7q
PubMed26625292
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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