Structure of PDB 6vtn Chain A Binding Site BS01

Receptor Information
>6vtn Chain A (length=375) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTN
IKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKP
RIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVS
IGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLK
NIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKE
IADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICE
MYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQ
IKRELNHLLYQRGYYNLKEAIGRKH
Ligand information
Ligand IDRL7
InChIInChI=1S/C17H16F4N2O/c1-9-11(8-22-15(9)16(24)23-13-4-5-13)6-10-2-3-12(7-14(10)18)17(19,20)21/h2-3,7-8,13,22H,4-6H2,1H3,(H,23,24)
InChIKeyHLDSAPKKTAWHGH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1c(Cc2ccc(cc2F)C(F)(F)F)c[nH]c1C(=O)NC3CC3
ACDLabs 12.01C(c1c(cc(cc1)C(F)(F)F)F)c3c(c(C(=O)NC2CC2)nc3)C
OpenEye OEToolkits 2.0.7Cc1c(c[nH]c1C(=O)NC2CC2)Cc3ccc(cc3F)C(F)(F)F
FormulaC17 H16 F4 N2 O
NameN-cyclopropyl-4-{[2-fluoro-4-(trifluoromethyl)phenyl]methyl}-3-methyl-1H-pyrrole-2-carboxamide
ChEMBLCHEMBL4635646
DrugBank
ZINC
PDB chain6vtn Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vtn Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		F171 L172 G181 H185 L187 F188 I263 R265 V532
Binding residue
(residue number reindexed from 1)		F10 L11 G20 H24 L26 F27 I102 R104 V341
Annotation score1
Binding affinityMOAD: ic50=0.044uM
Enzymatic activity
Catalytic site (original residue number in PDB) G248 N274 F278 S345 N347 T348 K429 N458
Catalytic site (residue number reindexed from 1) G87 N113 F117 S184 N186 T187 K238 N267
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
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Biological Process
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Cellular Component
External links
PDB RCSB:6vtn, PDBe:6vtn, PDBj:6vtn
PDBsum6vtn
PubMed32248693
UniProtQ08210|PYRD_PLAF7 Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=PFF0160c)

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