Structure of PDB 6l71 Chain A Binding Site BS04

Receptor Information

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

SQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTG
LYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFM
RLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRH
EYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFL
KVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGGMDF
DSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ

Ligand information

• Ligand ID: YDD
• InChI: InChI=1S/C29H51N5O14P2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-43-29-25(38)23(36)20(47-29)16-45-50(41,42)48-49(39,40)44-15-19-22(35)24(37)28(46-19)34-18-33-21-26(30)31-17-32-27(21)34/h17-20,22-25,28-29,35-38H,2-16H2,1H3,(H,39,40)(H,41,42)(H2,30,31,32)/t19-,20-,22-,23-,24-,25-,28-,29+/m1/s1
• InChIKey: XDVQERDQBQWVRC-UHUMEYFMSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCCO[C@@H]1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O)O
  CACTVS 3.385: CCCCCCCCCCCCCCO[C@H]1O[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](O)[C@H]1O
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCCOC1C(C(C(O1)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O)O
  CACTVS 3.385: CCCCCCCCCCCCCCO[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH](O)[CH]1O
• Formula: C29 H51 N5 O14 P2
• Name: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate
• PDB chain: 6l71 Chain C Residue 402

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): G84 G86 T89 D95 F96 R97 F119 L138 Q167 H187 F190 G261 T262 S263 N286 K287 E288 E323 C324
• Binding residue (residue number reindexed from 1): G32 G34 T37 D43 F44 R45 F67 L86 Q115 H135 F138 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)