Structure of PDB 4ej8 Chain A Binding Site BS01

Receptor Information

>4ej8 Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMNLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: 1F1
• InChI: InChI=1S/C9H7NO2/c11-9(12)7-2-1-6-3-4-10-8(6)5-7/h1-5,10H,(H,11,12)
• InChIKey: GHTDODSYDCPOCW-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.352: OC(=O)c1ccc2cc[nH]c2c1
  ACDLabs 11.02: O=C(O)c1ccc2c(c1)ncc2
  OpenEye OEToolkits 1.7.0: c1cc(cc2c1cc[nH]2)C(=O)O
• Formula: C9 H7 N O2
• Name: 1H-indole-6-carboxylic acid
• ChEMBL: CHEMBL1229732
• ZINC: ZINC000000058267
• PDB chain: 4ej8 Chain A Residue 106

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ej8 Small molecule regulation of protein conformation by binding in the Flap of HIV protease.
• Resolution: 2.347 Å
• Binding residue (original residue number in PDB): W42 P44 K45 K55
• Binding residue (residue number reindexed from 1): W42 P44 K45 K55
• Annotation score: 1
• Binding affinity: MOAD: Kd=4.1uM
  PDBbind-CN: -logKd/Ki=5.39,Kd=4.1uM

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• Catalytic site (residue number reindexed from 1): D25 T26 G27
• 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:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:4ej8, PDBe:4ej8, PDBj:4ej8
• PDBsum: 4ej8
• PubMed: 23540839
• UniProt: P12499|POL_HV1Z2 Gag-Pol polyprotein (Gene Name=gag-pol)