Structure of PDB 6l71 Chain A Binding Site BS03

Receptor Information

>6l71 Chain A (length=296) Species: 9606 (Homo sapiens)

SQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTG
LYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFM
RLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRH
EYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFL
KVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGGMDF
DSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ

Ligand information

• Ligand ID: YOY
• InChI: InChI=1S/C28H47N5O14P2/c1-2-3-4-5-6-7-8-9-10-11-12-19-45-24-22(35)18(44-28(24)46-19)14-42-49(39,40)47-48(37,38)41-13-17-21(34)23(36)27(43-17)33-16-32-20-25(29)30-15-31-26(20)33/h15-19,21-24,27-28,34-36H,2-14H2,1H3,(H,37,38)(H,39,40)(H2,29,30,31)/t17-,18+,19+,21-,22-,23-,24+,27-,28+/m1/s1
• InChIKey: KJBRVZZXXRAVKC-XBVYZWAMSA-N
• SMILES:
  CACTVS 3.385: CCCCCCCCCCCC[CH]1O[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O1
  CACTVS 3.385: CCCCCCCCCCCC[C@@H]1O[C@@H]2O[C@@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@@H]2O1
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCC[C@H]1O[C@H]2[C@@H]([C@@H](O[C@H]2O1)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCC1OC2C(C(OC2O1)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O
• Formula: C28 H47 N5 O14 P2
• Name: [[(2S,3aS,5S,6R,6aS)-2-dodecyl-6-oxidanyl-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
• PDB chain: 6l71 Chain C Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6l71 Sirtuin 2 protein with H3K18 myristoylated peptide
• Resolution: 2.109 Å
• Binding residue (original residue number in PDB): A85 G86 T89 D95 F96 R97 Q167 I169 H187 F190 F235 G261 T262 S263 N286 K287 E288 E323 C324
• Binding residue (residue number reindexed from 1): A33 G34 T37 D43 F44 R45 Q115 I117 H135 F138 F183 G209 T210 S211 N234 K235 E236 E264 C265
• 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): P42 D43 F44 R45 N116 D118 H135
• 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:6l71, PDBe:6l71, PDBj:6l71
• PDBsum: 6l71
• UniProt: Q8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)