Structure of PDB 1k6p Chain A Binding Site BS01

Receptor Information
>1k6p 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]
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF
Ligand information
Ligand IDXN3
InChIInChI=1S/C38H48N4O6/c1-38(2,3)40-37(46)31-23-41(21-26-13-14-33-34(18-26)48-24-47-33)15-16-42(31)22-29(43)19-28(17-25-9-5-4-6-10-25)36(45)39-35-30-12-8-7-11-27(30)20-32(35)44/h4-14,18,28-29,31-32,35,43-44H,15-17,19-24H2,1-3H3,(H,39,45)(H,40,46)/t28-,29+,31+,32-,35+/m1/s1
InChIKeyBJZTWVIYUGVEFV-OQOOGSQVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NC2c1ccccc1CC2O)C(Cc3ccccc3)CC(O)CN4C(C(=O)NC(C)(C)C)CN(CC4)Cc5ccc6OCOc6c5
OpenEye OEToolkits 1.5.0CC(C)(C)NC(=O)C1CN(CCN1CC(CC(Cc2ccccc2)C(=O)NC3c4ccccc4CC3O)O)Cc5ccc6c(c5)OCO6
OpenEye OEToolkits 1.5.0CC(C)(C)NC(=O)[C@@H]1C[N@@](CC[N@]1C[C@H](C[C@@H](Cc2ccccc2)C(=O)N[C@H]3c4ccccc4C[C@H]3O)O)Cc5ccc6c(c5)OCO6
CACTVS 3.341CC(C)(C)NC(=O)[CH]1CN(CCN1C[CH](O)C[CH](Cc2ccccc2)C(=O)N[CH]3[CH](O)Cc4ccccc34)Cc5ccc6OCOc6c5
CACTVS 3.341CC(C)(C)NC(=O)[C@@H]1CN(CCN1C[C@@H](O)C[C@@H](Cc2ccccc2)C(=O)N[C@@H]3[C@H](O)Cc4ccccc34)Cc5ccc6OCOc6c5
FormulaC38 H48 N4 O6
NameN-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(BENZO[1,3]DIOXOL-5-YLMETHYL)-PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE;
ANALOGUE OF INDINAVIR DRUG
ChEMBL
DrugBank
ZINCZINC000024531979
PDB chain1k6p Chain B Residue 807 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1k6p Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R8 D25 G27 G48 P81 T82
Binding residue
(residue number reindexed from 1)		R8 D25 G27 G48 P81 T82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.36,Kd=44nM
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:1k6p, PDBe:1k6p, PDBj:1k6p
PDBsum1k6p
PubMed11790852
UniProtP35963|POL_HV1Y2 Gag-Pol polyprotein (Gene Name=gag-pol)

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