Structure of PDB 1q1a Chain A Binding Site BS03

Receptor Information

>1q1a Chain A (length=285) Species: 4932 (Saccharomyces cerevisiae)

TASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHN
LARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQ
DKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQV
FKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLR
EKITTPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKAN
KRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA

Ligand information

• Ligand ID: OAD
• InChI: InChI=1S/C17H25N5O15P2/c1-6(23)34-13-11(25)8(36-17(13)27)3-33-39(30,31)37-38(28,29)32-2-7-10(24)12(26)16(35-7)22-5-21-9-14(18)19-4-20-15(9)22/h4-5,7-8,10-13,16-17,24-27H,2-3H2,1H3,(H,28,29)(H,30,31)(H2,18,19,20)/t7-,8-,10-,11-,12-,13-,16-,17+/m1/s1
• InChIKey: BFNOPXRXIQJDHO-DLFWLGJNSA-N
• SMILES:
  OpenEye OEToolkits 1.7.5: CC(=O)OC1C(C(OC1O)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O
  CACTVS 3.385: CC(=O)O[CH]1[CH](O)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH]1O
  ACDLabs 10.04: O=C(OC1C(O)C(OC1O)COP(=O)(O)OP(=O)(O)OCC4OC(n2c3ncnc(N)c3nc2)C(O)C4O)C
  OpenEye OEToolkits 1.7.5: CC(=O)O[C@@H]1[C@@H]([C@H](O[C@@H]1O)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
  CACTVS 3.385: CC(=O)O[C@H]1[C@@H](O)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@H]1O
• Formula: C17 H25 N5 O15 P2
• Name: 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE
• DrugBank: DB03478
• ZINC: ZINC000058638658
• PDB chain: 1q1a Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1q1a Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-Acetyl ADP ribose and histone peptide.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): G32 G34 T37 D43 F44 R45 Y52 Q115 H135 G223 T224 S225 N248 L249 Y269 S270
• Binding residue (residue number reindexed from 1): G28 G30 T33 D39 F40 R41 Y48 Q111 H131 G215 T216 S217 N240 L241 Y261 S262
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): P42 D43 F44 R45 N116 D118 H135
• Catalytic site (residue number reindexed from 1): P38 D39 F40 R41 N112 D114 H131
• 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:1q1a, PDBe:1q1a, PDBj:1q1a
• PDBsum: 1q1a
• PubMed: 14604530
• UniProt: P53686|HST2_YEAST NAD-dependent protein deacetylase HST2 (Gene Name=HST2)