Structure of PDB 8cbu Chain D Binding Site BS01

Receptor Information

>8cbu Chain D (length=142) Species: 11676 (Human immunodeficiency virus 1)

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFQGVIESMNKELKKIIGQ
VRDQAEHLKTAVQMAVFIHNKKRKGYSAGERIVDIIATDIQT

Ligand information

• Ligand ID: U60
• InChI: InChI=1S/C25H28O4/c1-14-5-10-20(16-6-7-16)23(22(14)24(25(26)27)29-17-8-9-17)19-11-12-21-18(15(19)2)4-3-13-28-21/h5,10-12,16-17,24H,3-4,6-9,13H2,1-2H3,(H,26,27)/t24-/m0/s1
• InChIKey: ZNMXSKRQRZHGAE-DEOSSOPVSA-N
• SMILES:
  CACTVS 3.385: Cc1ccc(C2CC2)c(c3ccc4OCCCc4c3C)c1[C@H](OC5CC5)C(O)=O
  OpenEye OEToolkits 2.0.7: Cc1ccc(c(c1[C@@H](C(=O)O)OC2CC2)c3ccc4c(c3C)CCCO4)C5CC5
  OpenEye OEToolkits 2.0.7: Cc1ccc(c(c1C(C(=O)O)OC2CC2)c3ccc4c(c3C)CCCO4)C5CC5
  CACTVS 3.385: Cc1ccc(C2CC2)c(c3ccc4OCCCc4c3C)c1[CH](OC5CC5)C(O)=O
• Formula: C25 H28 O4
• Name: (2S)-2-[3-cyclopropyl-6-methyl-2-(5-methyl-3,4-dihydro-2H-chromen-6-yl)phenyl]-2-cyclopropyloxy-ethanoic acid
• PDB chain: 8cbu Chain B Residue 505

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cbu Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase.
• Resolution: 2.44 Å
• Binding residue (original residue number in PDB): Q95 T125 A129 W132
• Binding residue (residue number reindexed from 1): Q39 T69 A73 W76
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.-
  2.7.7.49: RNA-directed DNA polymerase.
  2.7.7.7: DNA-directed DNA polymerase.
  3.1.-.-
  3.1.13.2: exoribonuclease H.
  3.1.26.13: retroviral ribonuclease H.
  3.4.23.16: HIV-1 retropepsin.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:8cbu, PDBe:8cbu, PDBj:8cbu
• PDBsum: 8cbu
• PubMed: 37310224
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)