Structure of PDB 6vlm Chain B Binding Site BS01

Receptor Information

>6vlm Chain B (length=149) Species: 11676 (Human immunodeficiency virus 1)

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTIHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVVESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRGYSAGERIVDIIATDIQT

Ligand information

• Ligand ID: R2D
• InChI: InChI=1S/C17H11ClN2O2S/c18-11-7-5-10(6-8-11)16-14(9-15(21)22)23-17-19-12-3-1-2-4-13(12)20(16)17/h1-8H,9H2,(H,21,22)
• InChIKey: PUYFLGQZLHVTHX-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1ccc2c(c1)nc3n2c(c(s3)CC(=O)O)c4ccc(cc4)Cl
  CACTVS 3.385: OC(=O)Cc1sc2nc3ccccc3n2c1c4ccc(Cl)cc4
  ACDLabs 12.01: c32n(c1ccccc1n2)c(c(CC(=O)O)s3)c4ccc(cc4)Cl
• Formula: C17 H11 Cl N2 O2 S
• Name: [3-(4-chlorophenyl)[1,3]thiazolo[3,2-a]benzimidazol-2-yl]acetic acid
• ChEMBL: CHEMBL2104737
• ZINC: ZINC000000002172
• PDB chain: 6vlm Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vlm Augmenting Hit Identification by Virtual Screening Techniques in Small Molecule Drug Discovery.
• Resolution: 2.32 Å
• Binding residue (original residue number in PDB): T125 A128 W132
• Binding residue (residue number reindexed from 1): T69 A72 W76
• Annotation score: 1
• Binding affinity: MOAD: ic50=10uM

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:6vlm, PDBe:6vlm, PDBj:6vlm
• PDBsum: 6vlm
• PubMed: 32309939
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)