Structure of PDB 1w5y Chain B Binding Site BS01

Receptor Information
>1w5y 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 IDBE6
InChIInChI=1S/C38H36F4N2O8/c39-23-9-11-27(41)21(13-23)17-51-35(37(49)43-31-25-7-3-1-5-19(25)15-29(31)45)33(47)34(48)36(52-18-22-14-24(40)10-12-28(22)42)38(50)44-32-26-8-4-2-6-20(26)16-30(32)46/h1-14,29-36,45-48H,15-18H2,(H,43,49)(H,44,50)/t29-,30-,31+,32+,33-,34-,35-,36-/m1/s1
InChIKeyMHRYDJWKKUNWJY-JQFCFGFHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc2c(c1)CC(C2NC(=O)C(C(C(C(C(=O)NC3c4ccccc4CC3O)OCc5cc(ccc5F)F)O)O)OCc6cc(ccc6F)F)O
CACTVS 3.341O[CH]1Cc2ccccc2[CH]1NC(=O)[CH](OCc3cc(F)ccc3F)[CH](O)[CH](O)[CH](OCc4cc(F)ccc4F)C(=O)N[CH]5[CH](O)Cc6ccccc56
CACTVS 3.341O[C@@H]1Cc2ccccc2[C@@H]1NC(=O)[C@H](OCc3cc(F)ccc3F)[C@H](O)[C@@H](O)[C@@H](OCc4cc(F)ccc4F)C(=O)N[C@@H]5[C@H](O)Cc6ccccc56
ACDLabs 10.04Fc1cc(c(F)cc1)COC(C(=O)NC3c2ccccc2CC3O)C(O)C(O)C(OCc4cc(F)ccc4F)C(=O)NC6c5ccccc5CC6O
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)OCc5cc(ccc5F)F)O)O)OCc6cc(ccc6F)F)O
FormulaC38 H36 F4 N2 O8
Name(2R,3R,4R,5R)-2,5-BIS[(2,5-DIFLUOROBENZYL)OXY]-3,4-DIHYDROXY-N,N'-BIS[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]HEXANEDIAMIDE;
HIV-1 INHIBITOR
ChEMBL
DrugBank
ZINCZINC000024692160
PDB chain1w5y 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

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PDB1w5y 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
Resolution1.9 Å
Binding residue
(original residue number in PDB)		R8 D25 G27 A28 D29 D30 G48 G49 I50 V82
Binding residue
(residue number reindexed from 1)		R8 D25 G27 A28 D29 D30 G48 G49 I50 V82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.48,Ki=3.3nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:1w5y, PDBe:1w5y, PDBj:1w5y
PDBsum1w5y
PubMed15560801
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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