Structure of PDB 5dy5 Chain A Binding Site BS03

Receptor Information

>5dy5 Chain A (length=300) Species: 9606 (Homo sapiens)

GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTG
LYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFM
RLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRH
EYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFL
KVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSGMIMGLGGG
MDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Ligand information

• Ligand ID: BU3
• InChI: InChI=1S/C4H10O2/c1-3(5)4(2)6/h3-6H,1-2H3/t3-,4-/m1/s1
• InChIKey: OWBTYPJTUOEWEK-QWWZWVQMSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@H]([C@@H](C)O)O
  CACTVS 3.341: C[C@@H](O)[C@@H](C)O
  ACDLabs 10.04: OC(C)C(O)C
  OpenEye OEToolkits 1.5.0: CC(C(C)O)O
  CACTVS 3.341: C[CH](O)[CH](C)O
• Formula: C4 H10 O2
• Name: (R,R)-2,3-BUTANEDIOL
• ZINC: ZINC000000901616
• PDB chain: 5dy5 Chain A Residue 405

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dy5 Structure-Based Development of an Affinity Probe for Sirtuin 2.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): A85 D95 F96 R97 N168 I169
• Binding residue (residue number reindexed from 1): A33 D43 F44 R45 N116 I117
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): P94 D95 F96 R97 N168 D170 H187
• Catalytic site (residue number reindexed from 1): P42 D43 F44 R45 N116 D118 H135
• 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

External links

• PDB: RCSB:5dy5, PDBe:5dy5, PDBj:5dy5
• PDBsum: 5dy5
• PubMed: 26748890
• UniProt: Q8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)