Structure of PDB 1npa Chain A Binding Site BS01

Receptor Information

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

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 3NH
• InChI: InChI=1S/C36H43N3O7/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/h1-14,26,28-32,34,38,40,42H,15-22,37H2,(H,39,43)/t26-,28-,29-,30-,31+,32+,34-,36-/m0/s1
• InChIKey: BYWKHOXUUACYRY-RJAVELRTSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CC(C(CC2(C(=O)C(CN2)C3c4ccccc4CC3OC(N)O)Cc5ccccc5)O)NC(=O)OC6CCOC6
  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(N)O)Cc5ccccc5)O)NC(=O)OC6CCOC6
  CACTVS 3.341: N[C@@H](O)O[C@@H]1Cc2ccccc2[C@@H]1[C@@H]3CN[C@](C[C@H](O)[C@H](Cc4ccccc4)NC(=O)O[C@H]5CCOC5)(Cc6ccccc6)C3=O
  CACTVS 3.341: N[CH](O)O[CH]1Cc2ccccc2[CH]1[CH]3CN[C](C[CH](O)[CH](Cc4ccccc4)NC(=O)O[CH]5CCOC5)(Cc6ccccc6)C3=O
  ACDLabs 10.04: O=C(OC1CCOC1)NC(Cc2ccccc2)C(O)CC5(C(=O)C(C4c3ccccc3CC4OC(O)N)CN5)Cc6ccccc6
• Formula: C36 H43 N3 O7
• Name: (3S)-TETRAHYDROFURAN-3-YL (1R,2S)-3-[4-((1R)-2-{[(S)-AMINO(HYDROXY)METHYL]OXY}-2,3-DIHYDRO-1H-INDEN-1-YL)-2-BENZYL-3-OXOPYRROLIDIN-2-YL]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
• DrugBank: DB01824
• PDB chain: 1npa Chain A Residue 100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1npa An orally bioavailable pyrrolinone inhibitor of HIV-1 protease: computational analysis and X-ray crystal structure of the enzyme complex.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 V32 G48 G49 I50 V82
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 V32 G48 G49 I50 V82
• Annotation score: 1
• Binding affinity: MOAD: ic50=2nM
  PDBbind-CN: -logKd/Ki=8.70,IC50=2.0nM

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:1npa, PDBe:1npa, PDBj:1npa
• PDBsum: 1npa
• PubMed: 9258349
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)