Structure of PDB 5jfp Chain A Binding Site BS01

Receptor Information

>5jfp Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: 6KK
• InChI: InChI=1S/C32H48N2O8S/c1-20(2)17-34(43(37,38)25-6-4-24(39-3)5-7-25)18-28(35)27(16-32-13-21-10-22(14-32)12-23(11-21)15-32)33-31(36)42-29-19-41-30-26(29)8-9-40-30/h4-7,20-23,26-30,35H,8-19H2,1-3H3,(H,33,36)/t21-,22+,23-,26-,27-,28+,29-,30+,32-/m0/s1
• InChIKey: ZMOFGDZIKIFMEU-JTPLMOPKSA-N
• SMILES:
  OpenEye OEToolkits 2.0.4: CC(C)CN(CC(C(CC12CC3CC(C1)CC(C3)C2)NC(=O)OC4COC5C4CCO5)O)S(=O)(=O)c6ccc(cc6)OC
  OpenEye OEToolkits 2.0.4: CC(C)CN(C[C@H]([C@H](CC12CC3CC(C1)CC(C3)C2)NC(=O)O[C@H]4CO[C@@H]5[C@H]4CCO5)O)S(=O)(=O)c6ccc(cc6)OC
  CACTVS 3.385: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](CC23CC4CC(CC(C4)C2)C3)NC(=O)O[C@H]5CO[C@H]6OCC[C@@H]56
  CACTVS 3.385: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](CC23CC4CC(CC(C4)C2)C3)NC(=O)O[CH]5CO[CH]6OCC[CH]56
  ACDLabs 12.01: c1(ccc(cc1)S(=O)(N(CC(O)C(NC(OC2COC3OCCC23)=O)CC64CC5CC(C4)CC(C5)C6)CC(C)C)=O)OC
• Formula: C32 H48 N2 O8 S
• Name: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]butan-2-yl}carbamate
• PDB chain: 5jfp Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jfp Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation.
• Resolution: 1.49 Å
• Binding residue (original residue number in PDB): D25 A28 D30 V82 I84
• Binding residue (residue number reindexed from 1): D25 A28 D30 V82 I84
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.32,Ki=0.48nM

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:5jfp, PDBe:5jfp, PDBj:5jfp
• PDBsum: 5jfp
• PubMed: 27389367
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)