Structure of PDB 8akd Chain B Binding Site BS01

Receptor Information

>8akd Chain B (length=277) Species: 9606 (Homo sapiens)

KGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDF
RGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQN
VDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGR
LCTVACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRP
SGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGL
EIPAWDGPRVLERALPPLPRPPTPKLE

Ligand information

• Ligand ID: AR6
• 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-ZQSHOCFMSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: 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
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)N
  ACDLabs 12.01: O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O
  CACTVS 3.370: 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
  CACTVS 3.370: 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
• Formula: C15 H23 N5 O14 P2
• Name: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE;
  Adenosine-5-Diphosphoribose
• DrugBank: DB02059
• ZINC: ZINC000014880207
• PDB chain: 8akd Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8akd Development of novel Sirtuin 6 inhibitors and activators based on a protein crystallography-based fragment screen
• Resolution: 1.76 Å
• Binding residue (original residue number in PDB): G52 A53 G54 T57 D63 F64 R65 Q113 H133 G214 T215 S216 I219 N240 L241 Q242 Y257 V258
• Binding residue (residue number reindexed from 1): G38 A39 G40 T43 D49 F50 R51 Q99 H119 G193 T194 S195 I198 N219 L220 Q221 Y236 V237
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 2.3.1.-
  2.3.1.286: protein acetyllysine N-acetyltransferase.
  2.4.2.-

Gene Ontology

Molecular Function

• GO:0070403 NAD+ binding

External links

• PDB: RCSB:8akd, PDBe:8akd, PDBj:8akd
• PDBsum: 8akd
• UniProt: Q8N6T7|SIR6_HUMAN NAD-dependent protein deacylase sirtuin-6 (Gene Name=SIRT6)