Structure of PDB 1w5v Chain B Binding Site BS01

Receptor Information
>1w5v Chain B (length=99) Species: 12721 (Human immunodeficiency virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDBE3
InChIInChI=1S/C38H38F2N2O8/c39-25-11-5-7-21(15-25)19-49-35(37(47)41-31-27-13-3-1-9-23(27)17-29(31)43)33(45)34(46)36(50-20-22-8-6-12-26(40)16-22)38(48)42-32-28-14-4-2-10-24(28)18-30(32)44/h1-16,29-36,43-46H,17-20H2,(H,41,47)(H,42,48)/t29-,30-,31+,32+,33-,34-,35-,36-/m1/s1
InChIKeyFSNSRNCFARXZOP-JQFCFGFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[C@@H]1Cc2ccccc2[C@@H]1NC(=O)[C@H](OCc3cccc(F)c3)[C@H](O)[C@@H](O)[C@@H](OCc4cccc(F)c4)C(=O)N[C@@H]5[C@H](O)Cc6ccccc56
ACDLabs 10.04Fc1cccc(c1)COC(C(=O)NC3c2ccccc2CC3O)C(O)C(O)C(OCc4cccc(F)c4)C(=O)NC6c5ccccc5CC6O
CACTVS 3.341O[CH]1Cc2ccccc2[CH]1NC(=O)[CH](OCc3cccc(F)c3)[CH](O)[CH](O)[CH](OCc4cccc(F)c4)C(=O)N[CH]5[CH](O)Cc6ccccc56
OpenEye OEToolkits 1.5.0c1ccc2c(c1)CC(C2NC(=O)C(C(C(C(C(=O)NC3c4ccccc4CC3O)OCc5cccc(c5)F)O)O)OCc6cccc(c6)F)O
OpenEye OEToolkits 1.5.0c1ccc2c(c1)C[C@H]([C@H]2NC(=O)[C@@H]([C@@H]([C@H]([C@H](C(=O)N[C@H]3c4ccccc4C[C@H]3O)OCc5cccc(c5)F)O)O)OCc6cccc(c6)F)O
FormulaC38 H38 F2 N2 O8
NameN,N-[2,5-O-DI-3-FLUORO-BENZYL-GLUCARYL]-DI-[1-AMINO-INDAN-2-OL];
INHIBITOR BEA403
ChEMBL
DrugBank
ZINCZINC000024691918
PDB chain1w5v Chain A Residue 1100 [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]
PDB1w5v Symmetric Fluoro-Substituted Diol-Based HIV Protease Inhibitors. Ortho-Fluorinated and Meta-Fluorinated P1/P1'-Benzyloxy Side Groups Significantly Improve the Antiviral Activity and Preserve Binding Efficacy
Resolution1.8 Å
Binding residue
(original residue number in PDB)		R8 L23 D25 G27 A28 D29 D30 V32 G48 G49 P81 V82
Binding residue
(residue number reindexed from 1)		R8 L23 D25 G27 A28 D29 D30 V32 G48 G49 P81 V82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.15,Ki=7.1nM
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:1w5v, PDBe:1w5v, PDBj:1w5v
PDBsum1w5v
PubMed15560801
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]