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BioLiP

Structure of PDB 5d7p Chain B Binding Site BS03

Receptor Information
>5d7p Chain B (length=299) 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
GMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDA
Ligand information
Ligand IDOCZ
InChIInChI=1S/C13H13ClN2O/c14-7-4-5-11-10(6-7)8-2-1-3-9(13(15)17)12(8)16-11/h4-6,9,16H,1-3H2,(H2,15,17)/t9-/m0/s1
InChIKeyFUZYTVDVLBBXDL-VIFPVBQESA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=O)[C@H]1CCCc2c1[nH]c3ccc(Cl)cc23
CACTVS 3.385NC(=O)[CH]1CCCc2c1[nH]c3ccc(Cl)cc23
OpenEye OEToolkits 1.9.2c1cc2c(cc1Cl)c3c([nH]2)[C@H](CCC3)C(=O)N
OpenEye OEToolkits 1.9.2c1cc2c(cc1Cl)c3c([nH]2)C(CCC3)C(=O)N
ACDLabs 12.01Clc1cc2c(cc1)nc3c2CCCC3C(=O)N
FormulaC13 H13 Cl N2 O
Name(1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide
ChEMBLCHEMBL597477
DrugBank
ZINCZINC000000093985
PDB chain5d7p 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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PDB5d7p Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
Resolution1.76 Å
Binding residue
(original residue number in PDB)		F131 A135 L138 Y139 G141 D170 F190
Binding residue
(residue number reindexed from 1)		F76 A80 L83 Y84 G86 D115 F135
Annotation score1
Binding affinityMOAD: ic50=20uM
BindingDB: IC50=19600nM
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:5d7p, PDBe:5d7p, PDBj:5d7p
PDBsum5d7p
PubMed26625292
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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