Structure of PDB 1npv Chain B Binding Site BS01

Receptor Information

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

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: L27
• InChI: InChI=1S/C35H37N3O6/c39-31(30(17-23-9-3-1-4-10-23)38-34(42)44-25-15-16-43-22-25)19-35(18-24-11-5-2-6-12-24)32(40)29(21-37-35)28-20-36-33(41)27-14-8-7-13-26(27)28/h1-14,21,25,28,30-31,37,39H,15-20,22H2,(H,36,41)(H,38,42)/t25-,28+,30-,31-,35-/m0/s1
• InChIKey: BFWPVLSACSESSM-VHGZSVTHSA-N
• SMILES:
  CACTVS 3.341: O[C@@H](C[C@]1(Cc2ccccc2)NC=C([C@@H]3CNC(=O)c4ccccc34)C1=O)[C@H](Cc5ccccc5)NC(=O)O[C@H]6CCOC6
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)C[C@@H]([C@H](C[C@]2(C(=O)C(=CN2)[C@@H]3CNC(=O)c4c3cccc4)Cc5ccccc5)O)NC(=O)O[C@H]6CCOC6
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CC(C(CC2(C(=O)C(=CN2)C3CNC(=O)c4c3cccc4)Cc5ccccc5)O)NC(=O)OC6CCOC6
  CACTVS 3.341: O[CH](C[C]1(Cc2ccccc2)NC=C([CH]3CNC(=O)c4ccccc34)C1=O)[CH](Cc5ccccc5)NC(=O)O[CH]6CCOC6
  ACDLabs 10.04: O=C(OC1CCOC1)NC(Cc2ccccc2)C(O)CC3(C(=O)C(=CN3)C5c4ccccc4C(=O)NC5)Cc6ccccc6
• Formula: C35 H37 N3 O6
• Name: {1-BENZYL-3-[2-BENZYL-3-OXO-4-(1-OXO-1,2,3,4-TETRAHYDRO- ISOQUINOLIN-4-YL)-2,3-DIHYDRO-1H-PYRROL-2-YL]-2- HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER;
  LDC271 INHIBITOR
• ZINC: ZINC000100361354
• PDB chain: 1npv Chain A Residue 479

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1npv 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 A228 D230 G248 G249 I250 P281
• Binding residue (residue number reindexed from 1): D25 G27 A28 D30 G48 G49 I50 P81
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.24,IC50=5.7nM

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:1npv, PDBe:1npv, PDBj:1npv
• PDBsum: 1npv
• PubMed: 12723947
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)