Structure of PDB 1ec3 Chain A Binding Site BS01

Receptor Information
>1ec3 Chain A (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 IDMS3
InChIInChI=1S/C42H52N6O8/c1-27(2)33(39(51)45-23-31-19-11-13-21-43-31)47-41(53)37(55-25-29-15-7-5-8-16-29)35(49)36(50)38(56-26-30-17-9-6-10-18-30)42(54)48-34(28(3)4)40(52)46-24-32-20-12-14-22-44-32/h5-22,27-28,33-38,49-50H,23-26H2,1-4H3,(H,45,51)(H,46,52)(H,47,53)(H,48,54)/t33-,34-,35+,36+,37+,38+/m0/s1
InChIKeySVFLQOLSPWURCD-CXPJILFNSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)[C@H](NC(=O)[C@H](OCc1ccccc1)[C@H](O)[C@@H](O)[C@@H](OCc2ccccc2)C(=O)N[C@@H](C(C)C)C(=O)NCc3ccccn3)C(=O)NCc4ccccn4
OpenEye OEToolkits 1.5.0CC(C)C(C(=O)NCc1ccccn1)NC(=O)C(C(C(C(C(=O)NC(C(C)C)C(=O)NCc2ccccn2)OCc3ccccc3)O)O)OCc4ccccc4
CACTVS 3.341CC(C)[CH](NC(=O)[CH](OCc1ccccc1)[CH](O)[CH](O)[CH](OCc2ccccc2)C(=O)N[CH](C(C)C)C(=O)NCc3ccccn3)C(=O)NCc4ccccn4
ACDLabs 10.04O=C(NCc1ncccc1)C(NC(=O)C(OCc2ccccc2)C(O)C(O)C(OCc3ccccc3)C(=O)NC(C(=O)NCc4ncccc4)C(C)C)C(C)C
OpenEye OEToolkits 1.5.0CC(C)[C@@H](C(=O)NCc1ccccn1)NC(=O)[C@@H]([C@@H]([C@H]([C@H](C(=O)N[C@@H](C(C)C)C(=O)NCc2ccccn2)OCc3ccccc3)O)O)OCc4ccccc4
FormulaC42 H52 N6 O8
NameN,N-[2,5-O-DIBENZYL-GLUCARYL]-DI-[VALINYL-AMINOMETHANYL-PYRIDINE];
INHIBITOR MSA367
ChEMBL
DrugBankDB03803
ZINCZINC000096210382
PDB chain1ec3 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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PDB1ec3 Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors
Resolution1.8 Å
Binding residue
(original residue number in PDB)		R8 D25 G27 A28 D29 G48 G49 P81 V82 I84
Binding residue
(residue number reindexed from 1)		R8 D25 G27 A28 D29 G48 G49 P81 V82 I84
Annotation score1
Binding affinityMOAD: Ki=0.92nM
PDBbind-CN: -logKd/Ki=9.04,Ki=0.92nM
Enzymatic activity
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:1ec3, PDBe:1ec3, PDBj:1ec3
PDBsum1ec3
PubMed12694187
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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