Structure of PDB 1ec1 Chain B Binding Site BS01

Receptor Information
>1ec1 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]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDBEE
InChIInChI=1S/C40H50N4O8S2/c1-23(2)31(37(47)41-5)43-39(49)35(51-19-25-7-11-27(12-8-25)29-15-17-53-21-29)33(45)34(46)36(40(50)44-32(24(3)4)38(48)42-6)52-20-26-9-13-28(14-10-26)30-16-18-54-22-30/h7-18,21-24,31-36,45-46H,19-20H2,1-6H3,(H,41,47)(H,42,48)(H,43,49)(H,44,50)/t31-,32-,33+,34+,35+,36+/m0/s1
InChIKeyAJZAPEZJWWQJHC-UWNKZCSISA-N
SMILES
SoftwareSMILES
CACTVS 3.341CNC(=O)[CH](NC(=O)[CH](OCc1ccc(cc1)c2cscc2)[CH](O)[CH](O)[CH](OCc3ccc(cc3)c4cscc4)C(=O)N[CH](C(C)C)C(=O)NC)C(C)C
OpenEye OEToolkits 1.5.0CC(C)C(C(=O)NC)NC(=O)C(C(C(C(C(=O)NC(C(C)C)C(=O)NC)OCc1ccc(cc1)c2ccsc2)O)O)OCc3ccc(cc3)c4ccsc4
OpenEye OEToolkits 1.5.0CC(C)[C@@H](C(=O)NC)NC(=O)[C@@H]([C@@H]([C@H]([C@H](C(=O)N[C@@H](C(C)C)C(=O)NC)OCc1ccc(cc1)c2ccsc2)O)O)OCc3ccc(cc3)c4ccsc4
CACTVS 3.341CNC(=O)[C@@H](NC(=O)[C@H](OCc1ccc(cc1)c2cscc2)[C@H](O)[C@@H](O)[C@@H](OCc3ccc(cc3)c4cscc4)C(=O)N[C@@H](C(C)C)C(=O)NC)C(C)C
ACDLabs 10.04O=C(NC)C(NC(=O)C(OCc2ccc(c1ccsc1)cc2)C(O)C(O)C(OCc4ccc(c3ccsc3)cc4)C(=O)NC(C(=O)NC)C(C)C)C(C)C
FormulaC40 H50 N4 O8 S2
NameN,N-[2,5-O-[DI-4-THIOPHEN-3-YL-BENZYL]-GLUCARYL]-DI-[VALYL-AMIDO-METHANE];
INHIBITOR BEA409
ChEMBLCHEMBL127214
DrugBankDB04547
ZINCZINC000095548316
PDB chain1ec1 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ec1 Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D125 G127 A128 D129 G148 G149 P181 V182 I184
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 G48 G49 P81 V82 I84
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.92,Ki=1.20nM
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.
3.4.23.16: HIV-1 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:1ec1, PDBe:1ec1, PDBj:1ec1
PDBsum1ec1
PubMed12694187
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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