Structure of PDB 2od7 Chain A Binding Site BS03

Receptor Information

>2od7 Chain A (length=289) Species: 4932 (Saccharomyces cerevisiae)

MASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSP
GTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFH
YLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCG
KVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWL
NDSEWLREKIQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGD
FKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA

Ligand information

• Ligand ID: A1R
• InChI: InChI=1S/C15H24N6O12P2/c16-13-9-14(19-4-18-13)21(5-20-9)15-12(25)11(24)8(32-15)3-31-35(28,29)33-34(26,27)30-2-6-10(23)7(22)1-17-6/h4-8,10-12,15,17,22-25H,1-3H2,(H,26,27)(H,28,29)(H2,16,18,19)/t6-,7+,8-,10-,11-,12-,15-/m1/s1
• InChIKey: NDQDTBCXPOIQGT-UHNJQBFTSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(OCC1NCC(O)C1O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H](CN4)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(CN4)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4NC[CH](O)[CH]4O)[CH](O)[CH]3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]4NC[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
• Formula: C15 H24 N6 O12 P2
• Name: 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
• ChEMBL: CHEMBL1230692
• ZINC: ZINC000016052290
• PDB chain: 2od7 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2od7 Structural basis for nicotinamide inhibition and base exchange in sir2 enzymes.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G32 A33 G34 T37 F44 R45 E64 Q115 G223 T224 S225 N248 Y269 S270
• Binding residue (residue number reindexed from 1): G35 A36 G37 T40 F47 R48 E67 Q118 G219 T220 S221 N244 Y265 S266
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): P42 D43 F44 R45 N116 D118 H135
• Catalytic site (residue number reindexed from 1): P45 D46 F47 R48 N119 D121 H138
• 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

External links

• PDB: RCSB:2od7, PDBe:2od7, PDBj:2od7
• PDBsum: 2od7
• PubMed: 17289592
• UniProt: P53686|HST2_YEAST NAD-dependent protein deacetylase HST2 (Gene Name=HST2)