Structure of PDB 5d7p Chain A Binding Site BS02

Receptor Information

>5d7p Chain A (length=302) Species: 9606 (Homo sapiens)

HMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGL
YDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMR
LLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHE
YPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLK
VDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGL
GGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASID
AQ

Ligand information

• Ligand ID: AR6
• InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
• InChIKey: SRNWOUGRCWSEMX-ZQSHOCFMSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)N
  ACDLabs 12.01: O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
• Formula: C15 H23 N5 O14 P2
• Name: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE;
  Adenosine-5-Diphosphoribose
• DrugBank: DB02059
• ZINC: ZINC000014880207
• PDB chain: 5d7p Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d7p Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
• Resolution: 1.76 Å
• Binding residue (original residue number in PDB): G84 A85 G86 T89 D95 F96 R97 Q167 H187 F235 G261 T262 S263 N286 K287 E288 E323 C324
• Binding residue (residue number reindexed from 1): G31 A32 G33 T36 D42 F43 R44 Q114 H134 F182 G208 T209 S210 N233 K234 E235 E270 C271
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): P94 D95 F96 R97 N168 D170 H187
• Catalytic site (residue number reindexed from 1): P41 D42 F43 R44 N115 D117 H134
• 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:5d7p, PDBe:5d7p, PDBj:5d7p
• PDBsum: 5d7p
• PubMed: 26625292
• UniProt: Q8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)