Structure of PDB 6vlh Chain B Binding Site BS01

Receptor Information

>6vlh Chain B (length=136) Species: 11676 (Human immunodeficiency virus 1)

SSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVITGQETAYFLLKLAGRW
PVKTVHTDNGSNFTSTTVKAACEWAGIKQEFGNKELKKIIGQVRDQAEHL
KTAVQMAVFIHNKKRKGGIGGYSAGERIVDIIATDI

Ligand information

• Ligand ID: R2A
• InChI: InChI=1S/C46H39N3O8/c1-29-9-13-39-35(23-29)37(27-43(50)51)41(56-39)15-11-31-5-3-7-33(25-31)45(54)47-17-18-48-19-21-49(22-20-48)46(55)34-8-4-6-32(26-34)12-16-42-38(28-44(52)53)36-24-30(2)10-14-40(36)57-42/h3-10,13-14,23-26H,17-22,27-28H2,1-2H3,(H,47,54)(H,50,51)(H,52,53)
• InChIKey: FKZRCFVPEMPOMA-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1ccc2c(c1)c(c(o2)C#Cc3cccc(c3)C(=O)NCCN4CCN(CC4)C(=O)c5cccc(c5)C#Cc6c(c7cc(ccc7o6)C)CC(=O)O)CC(=O)O
  ACDLabs 12.01: c2(oc1ccc(cc1c2CC(O)=O)C)C#Cc7cc(C(N6CCN(CCNC(=O)c5cc(C#Cc4c(CC(O)=O)c3cc(C)ccc3o4)ccc5)CC6)=O)ccc7
  CACTVS 3.385: Cc1ccc2oc(C#Cc3cccc(c3)C(=O)NCCN4CCN(CC4)C(=O)c5cccc(c5)C#Cc6oc7ccc(C)cc7c6CC(O)=O)c(CC(O)=O)c2c1
• Formula: C46 H39 N3 O8
• Name: (2-{[3-(4-{2-[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzene-1-carbonyl)amino]ethyl}piperazine-1-carbonyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid
• PDB chain: 6vlh Chain B Residue 308

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vlh HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor
• Resolution: 2.036 Å
• Binding residue (original residue number in PDB): Q95 E96 Y99 L102 T125 A129 A169 E170 H171 T174
• Binding residue (residue number reindexed from 1): Q37 E38 Y41 L44 T67 A71 A97 E98 H99 T102
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.49: RNA-directed DNA polymerase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

Biological Process

• GO:0015074 DNA integration

External links

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