Structure of PDB 3a2o Chain B Binding Site BS01

Receptor Information
>3a2o 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]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDKNJ
InChIInChI=1S/C30H40N4O5S/c1-18(2)15-32-28(37)27-30(5,6)40-17-34(27)29(38)25(36)23(14-21-10-8-7-9-11-21)33-24(35)16-39-26-19(3)12-22(31)13-20(26)4/h7-13,23,25,27,36H,1,14-17,31H2,2-6H3,(H,32,37)(H,33,35)/t23-,25-,27+/m0/s1
InChIKeyYCDHYYBDJVMMOY-SCTDOJESSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1cc(cc(c1OCC(=O)NC(Cc2ccccc2)C(C(=O)N3CSC(C3C(=O)NCC(=C)C)(C)C)O)C)N
OpenEye OEToolkits 1.7.0Cc1cc(cc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O)N3CSC([C@H]3C(=O)NCC(=C)C)(C)C)O)C)N
CACTVS 3.370CC(=C)CNC(=O)[CH]1N(CSC1(C)C)C(=O)[CH](O)[CH](Cc2ccccc2)NC(=O)COc3c(C)cc(N)cc3C
CACTVS 3.370CC(=C)CNC(=O)[C@H]1N(CSC1(C)C)C(=O)[C@@H](O)[C@H](Cc2ccccc2)NC(=O)COc3c(C)cc(N)cc3C
ACDLabs 12.01O=C(NCC(=C)/C)C3N(C(=O)C(O)C(NC(=O)COc1c(cc(N)cc1C)C)Cc2ccccc2)CSC3(C)C
FormulaC30 H40 N4 O5 S
Name(4R)-3-[(2S,3S)-3-{[(4-amino-2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-5,5-dimethyl-N-(2-methylprop -2-en-1-yl)-1,3-thiazolidine-4-carboxamide;
KNI-1689
ChEMBLCHEMBL573975
DrugBank
ZINCZINC000003925732
PDB chain3a2o Chain B Residue 999 [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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PDB3a2o Small-sized human immunodeficiency virus type-1 protease inhibitors containing allophenylnorstatine to explore the S2' pocket.
Resolution0.88 Å
Binding residue
(original residue number in PDB)		D125 G127 A128 D129 D130 I147 G149 I150 I184
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 I47 G49 I50 I84
Annotation score1
Binding affinityMOAD: Ki=0.83nM
PDBbind-CN: -logKd/Ki=9.08,Ki=0.83nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3a2o, PDBe:3a2o, PDBj:3a2o
PDBsum3a2o
PubMed19954246
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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