Structure of PDB 2upj Chain B Binding Site BS01

Receptor Information

>2upj Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: U02
• InChI: InChI=1S/C33H38N2O6/c1-5-22(18-21-10-7-6-8-11-21)27-20-26(36)30(31(38)40-27)29(23-14-15-23)24-12-9-13-25(19-24)35-28(37)16-17-34-32(39)41-33(2,3)4/h6-15,19-20,22-23,29,36H,5,16-18H2,1-4H3,(H,34,39)(H,35,37)/t22-,29+/m1/s1
• InChIKey: OORLDLMDGJZAFM-MNNSJKJDSA-N
• SMILES:
  CACTVS 3.341: CC[C@H](Cc1ccccc1)C2=CC(=C([C@@H](C3C=C3)c4cccc(NC(=O)CCNC(=O)OC(C)(C)C)c4)C(=O)O2)O
  OpenEye OEToolkits 1.5.0: CCC(Cc1ccccc1)C2=CC(=C(C(=O)O2)C(c3cccc(c3)NC(=O)CCNC(=O)OC(C)(C)C)C4C=C4)O
  CACTVS 3.341: CC[CH](Cc1ccccc1)C2=CC(=C([CH](C3C=C3)c4cccc(NC(=O)CCNC(=O)OC(C)(C)C)c4)C(=O)O2)O
  OpenEye OEToolkits 1.5.0: CC[C@H](Cc1ccccc1)C2=CC(=C(C(=O)O2)[C@H](c3cccc(c3)NC(=O)CCNC(=O)OC(C)(C)C)C4C=C4)O
  ACDLabs 10.04: O=C1OC(=CC(O)=C1C(c2cccc(NC(=O)CCNC(=O)OC(C)(C)C)c2)C3C=C3)C(Cc4ccccc4)CC
• Formula: C33 H38 N2 O6
• Name: [2-(3-{[6-(1-BENZYL-PROPYL)-4-HYDROXY-2-OXO-2H-PYRAN-3-YL]-CYCLOPROPYL-METHYL}-PHENYLCARBAMOYL)-ETHYL]-CARBAMIC ACID TERT-BUTYL ESTER
• ZINC: ZINC000058638919
• PDB chain: 2upj Chain A Residue 100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2upj Structure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): D25 A28 D29 D30 G49 P81 V82
• Binding residue (residue number reindexed from 1): D25 A28 D29 D30 G49 P81 V82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.39,Ki=0.041uM

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:2upj, PDBe:2upj, PDBj:2upj
• PDBsum: 2upj
• PubMed: 7658450
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)