Structure of PDB 6vty Chain C Binding Site BS01

Receptor Information
>6vty Chain C (length=366) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHL
DFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFR
DVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKN
KDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIIL
SVKEEIDNLEKNNFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETN
IDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQI
PIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLL
YQRGYYNLKEAIGRKH
Ligand information
Ligand IDRLA
InChIInChI=1S/C17H18F3NO2/c1-4-23-16(22)15-10(2)14(11(3)21-15)9-12-5-7-13(8-6-12)17(18,19)20/h5-8,21H,4,9H2,1-3H3
InChIKeyPWRCYLHLZGCFQH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCOC(=O)c1[nH]c(C)c(Cc2ccc(cc2)C(F)(F)F)c1C
ACDLabs 12.01c1(ccc(cc1)Cc2c(nc(C(OCC)=O)c2C)C)C(F)(F)F
OpenEye OEToolkits 2.0.7CCOC(=O)c1c(c(c([nH]1)C)Cc2ccc(cc2)C(F)(F)F)C
FormulaC17 H18 F3 N O2
Nameethyl 3,5-dimethyl-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxylate
ChEMBLCHEMBL4642145
DrugBank
ZINC
PDB chain6vty Chain C Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vty Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		L172 G181 C184 H185 L187 F188 I263 R265 V532
Binding residue
(residue number reindexed from 1)		L7 G16 C19 H20 L22 F23 I98 R100 V332
Annotation score1
Binding affinityMOAD: ic50=0.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) N274 F278 S345 N347 T348 K429 N458
Catalytic site (residue number reindexed from 1) N109 F113 S180 N182 T183 K229 N258
Enzyme Commision number 1.3.5.2: dihydroorotate dehydrogenase (quinone).
Gene Ontology
Molecular Function
GO:0004152 dihydroorotate dehydrogenase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6vty, PDBe:6vty, PDBj:6vty
PDBsum6vty
PubMed32248693
UniProtQ08210|PYRD_PLAF7 Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=PFF0160c)

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