Structure of PDB 3mxd Chain B Binding Site BS01

Receptor Information
>3mxd Chain B (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 A28 D30 P81 V82
Binding residue
(residue number reindexed from 1)		D25 A28 D30 P81 V82
Annotation score1
Binding affinityPDBbind-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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