Structure of PDB 6vka Chain A Binding Site BS01

Receptor Information

>6vka Chain A (length=141) Species: 11676 (Human immunodeficiency virus 1)

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACEWAGIKQEFGIPESMNKELKKIIGQV
RDQAEHLKTAVQMAVFIHNKKRGGYSAGERIVDIIATDIET

Ligand information

• Ligand ID: QZV
• InChI: InChI=1S/C46H40N2O10/c1-29-3-15-39-35(25-29)37(27-43(49)50)41(57-39)17-9-31-5-11-33(12-6-31)45(53)47-19-21-55-23-24-56-22-20-48-46(54)34-13-7-32(8-14-34)10-18-42-38(28-44(51)52)36-26-30(2)4-16-40(36)58-42/h3-8,11-16,25-26H,19-24,27-28H2,1-2H3,(H,47,53)(H,48,54)(H,49,50)(H,51,52)
• InChIKey: PWEZNMFJKKNKMN-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1ccc2c(c1)c(c(o2)C#Cc3ccc(cc3)C(=O)NCCOCCOCCNC(=O)c4ccc(cc4)C#Cc5c(c6cc(ccc6o5)C)CC(=O)O)CC(=O)O
  ACDLabs 12.01: c6c(C#Cc2c(CC(O)=O)c1c(ccc(C)c1)o2)ccc(C(NCCOCCOCCNC(=O)c3ccc(cc3)C#Cc4oc5c(c4CC(O)=O)cc(cc5)C)=O)c6
  CACTVS 3.385: Cc1ccc2oc(C#Cc3ccc(cc3)C(=O)NCCOCCOCCNC(=O)c4ccc(cc4)C#Cc5oc6ccc(C)cc6c5CC(O)=O)c(CC(O)=O)c2c1
• Formula: C46 H40 N2 O10
• Name: 2,2'-{ethane-1,2-diylbis[oxyethane-2,1-diylcarbamoyl-4,1-phenyleneethyne-2,1-diyl(5-methyl-1-benzofuran-2,3-diyl)]}diacetic acid
• PDB chain: 6vka Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vka HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor
• Resolution: 1.863 Å
• Binding residue (original residue number in PDB): Q95 E96 Y99 T125 A129 A169 E170 H171 T174
• Binding residue (residue number reindexed from 1): Q39 E40 Y43 T69 A73 A104 E105 H106 T109
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.-

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:6vka, PDBe:6vka, PDBj:6vka
• PDBsum: 6vka
• UniProt: F2WR39