Structure of PDB 1szd Chain A Binding Site BS03

Receptor Information

>1szd Chain A (length=291) Species: 4932 (Saccharomyces cerevisiae)

MASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSP
GTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFH
YLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCG
KVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWL
NDSEWLREKITTQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETV
GDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA

Ligand information

• Ligand ID: APR
• 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-KEOHHSTQSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)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]([C@@H](O4)O)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(C(O4)O)O)O)O)O)N
  CACTVS 3.341: 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
  CACTVS 3.341: 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
• Formula: C15 H23 N5 O14 P2
• Name: ADENOSINE-5-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL1231026
• ZINC: ZINC000017654550
• PDB chain: 1szd Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1szd Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): G32 A33 G34 F44 R45 E64 Q115 F184 G223 T224 S225 V228 N248 L249 Y269 S270
• Binding residue (residue number reindexed from 1): G35 A36 G37 F47 R48 E67 Q118 F187 G221 T222 S223 V226 N246 L247 Y267 S268
• Annotation score: 3
• Binding affinity: MOAD: Kd=29.16uM
  PDBbind-CN: -logKd/Ki=4.54,Kd=29.16uM

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:1szd, PDBe:1szd, PDBj:1szd
• PDBsum: 1szd
• PubMed: 15150415
• UniProt: P53686|HST2_YEAST NAD-dependent protein deacetylase HST2 (Gene Name=HST2)