Structure of PDB 1npw Chain B Binding Site BS01

Receptor Information

>1npw Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: LGZ
• InChI: InChI=1S/C36H39N3O7/c37-34(42)46-31-18-25-13-7-8-14-27(25)32(31)28-21-38-36(33(28)41,19-24-11-5-2-6-12-24)20-30(40)29(17-23-9-3-1-4-10-23)39-35(43)45-26-15-16-44-22-26/h1-14,21,26,29-32,38,40H,15-20,22H2,(H2,37,42)(H,39,43)/t26-,29+,30+,31-,32-,36+/m1/s1
• InChIKey: LIIUTXFOEDWJEK-HQJNJJHVSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)C[C@@H]([C@H](C[C@]2(C(=O)C(=CN2)[C@H]3c4ccccc4C[C@H]3OC(=O)N)Cc5ccccc5)O)NC(=O)OC6CCOC6
  CACTVS 3.341: NC(=O)O[CH]1Cc2ccccc2[CH]1C3=CN[C](C[CH](O)[CH](Cc4ccccc4)NC(=O)O[CH]5CCOC5)(Cc6ccccc6)C3=O
  CACTVS 3.341: NC(=O)O[C@@H]1Cc2ccccc2[C@@H]1C3=CN[C@](C[C@H](O)[C@H](Cc4ccccc4)NC(=O)O[C@@H]5CCOC5)(Cc6ccccc6)C3=O
  ACDLabs 10.04: O=C(OC1CCOC1)NC(Cc2ccccc2)C(O)CC3(C(=O)C(=CN3)C5c4ccccc4CC5OC(=O)N)Cc6ccccc6
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CC(C(CC2(C(=O)C(=CN2)C3c4ccccc4CC3OC(=O)N)Cc5ccccc5)O)NC(=O)OC6CCOC6
• Formula: C36 H39 N3 O7
• Name: CARBAMIC ACID 1-{5-BENZYL-5-[2-HYDROXY-4-PHENYL-3-(TETRAHYDRO-FURAN- 3-YLOXYCARBONYLAMINO)-BUTYL]-4-OXO-4,5-DIHYDRO-1H-PYRROL-3-YL}- INDAN-2-YL ESTER;
  LGZ479 INHIBITOR
• ZINC: ZINC000103548459
• PDB chain: 1npw Chain A Residue 479

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1npw Design, synthesis, and biological evaluation of monopyrrolinone-based HIV-1 protease inhibitors.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): D225 G227 D230 G249 P281 V282
• Binding residue (residue number reindexed from 1): D25 G27 D30 G49 P81 V82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.70,IC50=2.0nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D225 T226 G227
• 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:1npw, PDBe:1npw, PDBj:1npw
• PDBsum: 1npw
• PubMed: 12723947
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)