Structure of PDB 1hps Chain B Binding Site BS02

Receptor Information

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

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: RUN
• InChI: InChI=1S/C38H46N4O5/c1-25(2)34(42-38(46)47-24-29-18-12-7-13-19-29)37(45)41-31(21-28-16-10-6-11-17-28)33(43)22-30(20-27-14-8-5-9-15-27)36-39-23-32(40-36)35(44)26(3)4/h5-19,23,25-26,30-31,33-34,43H,20-22,24H2,1-4H3,(H,39,40)(H,41,45)(H,42,46)/t30-,31+,33+,34+/m1/s1
• InChIKey: RQAVEWKEUKIFLD-LVPKLHHISA-N
• SMILES:
  CACTVS 3.341: CC(C)[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](Cc2ccccc2)[C@@H](O)C[C@@H](Cc3ccccc3)c4[nH]c(cn4)C(=O)C(C)C
  ACDLabs 10.04: O=C(OCc1ccccc1)NC(C(=O)NC(C(O)CC(c2ncc(n2)C(=O)C(C)C)Cc3ccccc3)Cc4ccccc4)C(C)C
  OpenEye OEToolkits 1.5.0: CC(C)C(C(=O)NC(Cc1ccccc1)C(CC(Cc2ccccc2)c3[nH]c(cn3)C(=O)C(C)C)O)NC(=O)OCc4ccccc4
  OpenEye OEToolkits 1.5.0: CC(C)[C@@H](C(=O)N[C@@H](Cc1ccccc1)[C@H](C[C@@H](Cc2ccccc2)c3[nH]c(cn3)C(=O)C(C)C)O)NC(=O)OCc4ccccc4
  CACTVS 3.341: CC(C)[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](Cc2ccccc2)[CH](O)C[CH](Cc3ccccc3)c4[nH]c(cn4)C(=O)C(C)C
• Formula: C38 H46 N4 O5
• Name: 2-[(1R,3S,4S)-1-BENZYL-4-[N-(BENZYLOXYCARBONYL)-L-VALYL]AMINO-3-PHENYLPENTYL]-4(5)-(2-METHYLPROPIONYL)IMIDAZOLE;
  SB206343
• ChEMBL: CHEMBL326473
• PDB chain: 1hps Chain B Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1hps Rational design, synthesis, and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'--P2' amide bond isostere.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): R8 L23 D25 G27 A28 D29 D30 G48 G49 I50 V82
• Binding residue (residue number reindexed from 1): R8 L23 D25 G27 A28 D29 D30 G48 G49 I50 V82
• Annotation score: 1
• Binding affinity: MOAD: Ki=0.6nM
  PDBbind-CN: -logKd/Ki=9.22,Ki=0.6nM

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:1hps, PDBe:1hps, PDBj:1hps
• PDBsum: 1hps
• PubMed: 7932533
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)