Structure of PDB 5jfu Chain B Binding Site BS01

Receptor Information
>5jfu Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand ID6KQ
InChIInChI=1S/C35H46N2O8S/c1-42-27-7-9-28(10-8-27)46(40,41)37(20-23-5-3-2-4-6-23)21-31(38)30(19-35-16-24-13-25(17-35)15-26(14-24)18-35)36-34(39)45-32-22-44-33-29(32)11-12-43-33/h2-10,24-26,29-33,38H,11-22H2,1H3,(H,36,39)/t24-,25+,26-,29-,30-,31+,32-,33+,35-/m0/s1
InChIKeyVFCWWTCOEZADQB-VTBYYCNJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4COc1ccc(cc1)S(=O)(=O)N(Cc2ccccc2)CC(C(CC34CC5CC(C3)CC(C5)C4)NC(=O)OC6COC7C6CCO7)O
CACTVS 3.385COc1ccc(cc1)[S](=O)(=O)N(C[CH](O)[CH](CC23CC4CC(CC(C4)C2)C3)NC(=O)O[CH]5CO[CH]6OCC[CH]56)Cc7ccccc7
CACTVS 3.385COc1ccc(cc1)[S](=O)(=O)N(C[C@@H](O)[C@H](CC23CC4CC(CC(C4)C2)C3)NC(=O)O[C@H]5CO[C@H]6OCC[C@@H]56)Cc7ccccc7
ACDLabs 12.01c1(ccc(cc1)S(=O)(N(Cc2ccccc2)CC(O)C(CC53CC4CC(C3)CC(C4)C5)NC(OC7C6CCOC6OC7)=O)=O)OC
OpenEye OEToolkits 2.0.4COc1ccc(cc1)S(=O)(=O)N(Cc2ccccc2)C[C@H]([C@H](CC34CC5CC(C3)CC(C5)C4)NC(=O)O[C@H]6CO[C@@H]7[C@H]6CCO7)O
FormulaC35 H46 N2 O8 S
Name(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-4-{benzyl[(4-methoxyphenyl)sulfonyl]amino}-3-hydroxy-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]butan-2-yl}carbamate
ChEMBL
DrugBank
ZINC
PDB chain5jfu Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5jfu Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation.
Resolution1.7 Å
Binding residue
(original residue number in PDB)
D25 G27 A28 D29 G48 G49 I50 I84
Binding residue
(residue number reindexed from 1)
D25 G27 A28 D29 G48 G49 I50 I84
Annotation score1
Binding affinityMOAD: Ki=8.5nM
PDBbind-CN: -logKd/Ki=8.07,Ki=8.5nM
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

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5jfu, PDBe:5jfu, PDBj:5jfu
PDBsum5jfu
PubMed27389367
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]