Structure of PDB 6fky Chain A Binding Site BS04

Receptor Information
>6fky Chain A (length=262) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLTAFREHFAKAKHIAIITGAGVSAESGVPTFRGPGGFWRKWQAQDLATP
EAFSRDPSLVWEFYHYRREVMRSKMPNPAHLAIAECEARLGQQGRSVVII
TQNIDELHHRAGSKHVYEIHGSLFKTRCMSCGEVKANHKSPICPALDGKG
APDPNTKEARIPVELLPRCERKSCNGLLRPHVVWFGETLDSDILTAVERE
LEKCDLCLVVGTSSIVYPAAMFAPQVASRGVPVAEFNMECTPATQKYHFE
GPCGSTLPPALE
Ligand information
Ligand IDE9N
InChIInChI=1S/C11H12O4S/c12-10(13)6-9(11(14)15)16-7-8-4-2-1-3-5-8/h1-5,9H,6-7H2,(H,12,13)(H,14,15)/t9-/m1/s1
InChIKeyPLQQDQFONINWJP-SECBINFHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)CSC(CC(=O)O)C(=O)O
OpenEye OEToolkits 2.0.6c1ccc(cc1)CS[C@H](CC(=O)O)C(=O)O
CACTVS 3.385OC(=O)C[C@@H](SCc1ccccc1)C(O)=O
CACTVS 3.385OC(=O)C[CH](SCc1ccccc1)C(O)=O
FormulaC11 H12 O4 S
Name(2~{R})-2-(phenylmethylsulfanyl)butanedioic acid
ChEMBL
DrugBank
ZINC
PDB chain6fky Chain C Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fky Potent and Selective Inhibitors of Human Sirtuin 5.
Resolution2.98 Å
Binding residue
(original residue number in PDB)		T65 Y98 R101 Q136 N137 I138 H154 V216
Binding residue
(residue number reindexed from 1)		T31 Y64 R67 Q102 N103 I104 H120 V182
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.49,Ki=320nM
Enzymatic activity
Catalytic site (original residue number in PDB) P64 T65 F66 R67 N137 D139 H154
Catalytic site (residue number reindexed from 1) P30 T31 F32 R33 N103 D105 H120
Enzyme Commision number 2.3.1.-
Gene Ontology
Molecular Function
GO:0000035 acyl binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0017136 NAD-dependent histone deacetylase activity
GO:0034979 NAD-dependent protein lysine deacetylase activity
GO:0036054 protein-malonyllysine demalonylase activity
GO:0036055 protein-succinyllysine desuccinylase activity
GO:0046872 metal ion binding
GO:0061697 protein-glutaryllysine deglutarylase activity
GO:0070403 NAD+ binding
GO:1901363 heterocyclic compound binding
Biological Process
GO:0006338 chromatin remodeling
GO:0006476 protein deacetylation
GO:0010566 regulation of ketone biosynthetic process
GO:0036047 peptidyl-lysine demalonylation
GO:0036048 protein desuccinylation
GO:0036049 peptidyl-lysine desuccinylation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6fky, PDBe:6fky, PDBj:6fky
PDBsum6fky
PubMed29494161
UniProtQ6DHI5|SIR5_DANRE NAD-dependent protein deacylase sirtuin-5, mitochondrial (Gene Name=sirt5)

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