Structure of PDB 5ytk Chain C Binding Site BS03

Receptor Information
>5ytk Chain C (length=273) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQY
DLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGL
LLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRAD
VMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTS
LEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVE
SLVELLGWTEEMRDLVQRETGKL
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain5ytk Chain C 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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PDB5ytk Sensing and Transmitting Intracellular Amino Acid Signals through Reversible Lysine Aminoacylations
Resolution2.7 Å
Binding residue
(original residue number in PDB)
G295 E296
Binding residue
(residue number reindexed from 1)
G174 E175
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) P155 D156 F157 R158 N229 D231 H248
Catalytic site (residue number reindexed from 1) P34 D35 F36 R37 N108 D110 H127
Enzyme Commision number 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:5ytk, PDBe:5ytk, PDBj:5ytk
PDBsum5ytk
PubMed29198988
UniProtQ9NTG7|SIR3_HUMAN NAD-dependent protein deacetylase sirtuin-3, mitochondrial (Gene Name=SIRT3)

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