Structure of PDB 3ec0 Chain B Binding Site BS01

Receptor Information
>3ec0 Chain B (length=99) Species: 11720 (Human immunodeficiency virus type 2 (ISOLATE ROD)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGI
GGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL
Ligand information
Ligand IDGRL
InChIInChI=1S/C29H40N2O7S/c1-20(2)17-31(39(35,36)25-10-8-22(19-32)9-11-25)18-27(33)26(14-21-6-4-3-5-7-21)30-29(34)38-24-15-23-12-13-37-28(23)16-24/h3-11,20,23-24,26-28,32-33H,12-19H2,1-2H3,(H,30,34)/t23-,24+,26-,27+,28+/m0/s1
InChIKeyVYBDPVQMILRSMK-GRXYLYAXSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2C[CH]3CCO[CH]3C2)[S](=O)(=O)c4ccc(CO)cc4
CACTVS 3.341CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@@H]2C[C@@H]3CCO[C@@H]3C2)[S](=O)(=O)c4ccc(CO)cc4
OpenEye OEToolkits 1.5.0CC(C)CN(C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@@H]2C[C@@H]3CCO[C@@H]3C2)O)S(=O)(=O)c4ccc(cc4)CO
ACDLabs 10.04O=S(=O)(c1ccc(cc1)CO)N(CC(C)C)CC(O)C(NC(=O)OC3CC2C(OCC2)C3)Cc4ccccc4
OpenEye OEToolkits 1.5.0CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2CC3CCOC3C2)O)S(=O)(=O)c4ccc(cc4)CO
FormulaC29 H40 N2 O7 S
Name(3AS,5R,6AR)-HEXAHYDRO-2H-CYCLOPENTA[B]FURAN-5-YL (2S,3S)-3-HYDROXY-4-(4-(HYDROXYMETHYL)-N-ISOBUTYLPHENYLSULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE
ChEMBLCHEMBL254349
DrugBank
ZINCZINC000014954111
PDB chain3ec0 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ec0 Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease
Resolution1.18 Å
Binding residue
(original residue number in PDB)		D125 G127 A128 D129 V147 G148 G149 I150 I182
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 V47 G48 G49 I50 I82
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D125 T126 G127
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.
3.4.23.47: HIV-2 retropepsin.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:3ec0, PDBe:3ec0, PDBj:3ec0
PDBsum3ec0
PubMed18834890
UniProtP04584|POL_HV2RO Gag-Pol polyprotein (Gene Name=gag-pol)

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