Structure of PDB 1eby Chain B Binding Site BS01

Receptor Information

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

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: BEB
• InChI: InChI=1S/C38H40N2O8/c41-29-19-25-15-7-9-17-27(25)31(29)39-37(45)35(47-21-23-11-3-1-4-12-23)33(43)34(44)36(48-22-24-13-5-2-6-14-24)38(46)40-32-28-18-10-8-16-26(28)20-30(32)42/h1-18,29-36,41-44H,19-22H2,(H,39,45)(H,40,46)/t29-,30-,31+,32+,33-,34-,35-,36-/m1/s1
• InChIKey: UOHMQWQGAJAUGT-JQFCFGFHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)COC(C(C(C(C(=O)NC2c3ccccc3CC2O)OCc4ccccc4)O)O)C(=O)NC5c6ccccc6CC5O
  CACTVS 3.341: O[CH]1Cc2ccccc2[CH]1NC(=O)[CH](OCc3ccccc3)[CH](O)[CH](O)[CH](OCc4ccccc4)C(=O)N[CH]5[CH](O)Cc6ccccc56
  ACDLabs 10.04: O=C(NC2c1ccccc1CC2O)C(OCc3ccccc3)C(O)C(O)C(OCc4ccccc4)C(=O)NC6c5ccccc5CC6O
  CACTVS 3.341: O[C@@H]1Cc2ccccc2[C@@H]1NC(=O)[C@H](OCc3ccccc3)[C@H](O)[C@@H](O)[C@@H](OCc4ccccc4)C(=O)N[C@@H]5[C@H](O)Cc6ccccc56
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CO[C@H]([C@@H]([C@H]([C@H](C(=O)N[C@H]2c3ccccc3C[C@H]2O)OCc4ccccc4)O)O)C(=O)N[C@H]5c6ccccc6C[C@H]5O
• Formula: C38 H40 N2 O8
• Name: N,N-[2,5-O-DIBENZYL-GLUCARYL]-DI-[1-AMINO-INDAN-2-OL];
  INHIBITOR BEA369
• ChEMBL: CHEMBL367384
• ZINC: ZINC000004424152
• PDB chain: 1eby Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1eby Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors
• Resolution: 2.294 Å
• Binding residue (original residue number in PDB): D125 G127 A128 D129 D130 V132 G148 P181 V182
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 D30 V32 G48 P81 V82
• Annotation score: 1
• Binding affinity: MOAD: Ki=0.2nM
  PDBbind-CN: -logKd/Ki=9.70,Ki=0.20nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D125 T126 G127
• 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:1eby, PDBe:1eby, PDBj:1eby
• PDBsum: 1eby
• PubMed: 12694187
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)