Structure of PDB 3mxd Chain A Binding Site BS01

Receptor Information
>3mxd Chain A (length=99) Species: 11685 (HIV-1 M:B_ARV2/SF2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDK53
InChIInChI=1S/C31H35N3O9S/c1-20(2)16-33(44(39,40)22-12-13-27-28(15-22)42-19-41-27)17-26(36)23(14-21-8-4-3-5-9-21)32-30(37)29-18-34(31(38)43-29)24-10-6-7-11-25(24)35/h3-13,15,20,23,26,29,35-36H,14,16-19H2,1-2H3,(H,32,37)/t23-,26+,29-/m0/s1
InChIKeyACRHTKSQCOUKAC-LBGGBARHSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)[CH]2CN(C(=O)O2)c3ccccc3O)[S](=O)(=O)c4ccc5OCOc5c4
ACDLabs 12.01O=C(NC(Cc1ccccc1)C(O)CN(CC(C)C)S(=O)(=O)c3cc2OCOc2cc3)C5OC(=O)N(c4c(O)cccc4)C5
OpenEye OEToolkits 1.7.0CC(C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)[C@@H]2CN(C(=O)O2)c3ccccc3O)O)S(=O)(=O)c4ccc5c(c4)OCO5
CACTVS 3.370CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@H]2CN(C(=O)O2)c3ccccc3O)[S](=O)(=O)c4ccc5OCOc5c4
OpenEye OEToolkits 1.7.0CC(C)CN(CC(C(Cc1ccccc1)NC(=O)C2CN(C(=O)O2)c3ccccc3O)O)S(=O)(=O)c4ccc5c(c4)OCO5
FormulaC31 H35 N3 O9 S
Name(5S)-N-{(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl}-3-(2-hydroxyphenyl)-2 -oxo-1,3-oxazolidine-5-carboxamide;
(5S)-N-[(1S,2R)-3-[(1,3-Benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-2-hydroxy-1-(phenylmethyl)propyl]-3-(2-hydroxyp henyl)-2-oxooxazolidine-5-carboxamide
ChEMBLCHEMBL1233803
DrugBank
ZINCZINC000058638736
PDB chain3mxd Chain A Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3mxd Structure-Based Design, Synthesis, and Structure-Activity Relationship Studies of HIV-1 Protease Inhibitors Incorporating Phenyloxazolidinones.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 D30 I47 G48 I50
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 I47 G48 I50
Annotation score1
Binding affinityMOAD: Ki=1.47nM
PDBbind-CN: -logKd/Ki=8.83,Ki=1.47nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3mxd, PDBe:3mxd, PDBj:3mxd
PDBsum3mxd
PubMed20958050
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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