Structure of PDB 5ojn Chain A Binding Site BS02

Receptor Information

>5ojn Chain A (length=272) Species: 8364 (Xenopus tropicalis)

HMVPACPPPNPHQVEQLQDFVSQSQRLFVMTGAGISTESGIPDYRSEGVG
LYSRTERRPIQHSEFVQSQAARRRYWARNFVGWPSFSSHEPNSAHVNLCK
WERAGRLHWLVTQNVDALHTKAGQCRLSELHGCTHRVICLGCQTVTKRSE
LQERFLNLNPSWNELTDEQVSDFQVPACTKCGGILKPQVTFFGDTVNRGF
VFSIYEQMKQADAMLIVGSSLQVYSGYRFALNAKELHLPIAILNIGPTRA
DHLAKVKVSARCGDVLPHILLQ

Ligand information

• Ligand ID: 9X8
• InChI: InChI=1S/C17H25N5O14P2S/c1-6(39)33-13-11(24)8(35-17(13)26)3-32-38(29,30)36-37(27,28)31-2-7-10(23)12(25)16(34-7)22-5-21-9-14(18)19-4-20-15(9)22/h4-5,7-8,10-13,16-17,23-26H,2-3H2,1H3,(H,27,28)(H,29,30)(H2,18,19,20)/t7-,8-,10-,11-,12-,13-,16-,17+/m1/s1
• InChIKey: KCGNVGFYYIVLLI-DLFWLGJNSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(=S)O[C@@H]1[C@@H]([C@H](O[C@@H]1O)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
  CACTVS 3.385: CC(=S)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
  OpenEye OEToolkits 2.0.6: CC(=S)OC1C(C(OC1O)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O
  CACTVS 3.385: CC(=S)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 O14 P2 S
• Name: thioacetyl-ADP-ribose
• PDB chain: 5ojn Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ojn Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): P33 G61 A62 G63 T66 E67 D72 Y73 R74 S75 Q142 H160 G259 S260 S261 V264 N285 I286 G287 R302 C303
• Binding residue (residue number reindexed from 1): P4 G32 A33 G34 T37 E38 D43 Y44 R45 S46 Q113 H131 G218 S219 S220 V223 N244 I245 G246 R261 C262
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): P71 D72 Y73 R74 N143 D145 H160
• Catalytic site (residue number reindexed from 1): P42 D43 Y44 R45 N114 D116 H131
• Enzyme Commision number: 2.3.1.-
  2.3.1.286: protein acetyllysine N-acetyltransferase.

Gene Ontology

Molecular Function

• GO:0034979 NAD-dependent protein lysine deacetylase activity
• GO:0051287 NAD binding
• GO:0070403 NAD+ binding

External links

• PDB: RCSB:5ojn, PDBe:5ojn, PDBj:5ojn
• PDBsum: 5ojn
• PubMed: 29138502
• UniProt: Q28CB4