Structure of PDB 7kyy Chain D Binding Site BS01

Receptor Information
>7kyy Chain D (length=371) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACT
NIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAK
PRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGV
SIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKL
KNIILSVKEEIDNLEKNNFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADV
LLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNY
TNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRE
LNHLLYQRGYYNLKEAIGRKH
Ligand information
Ligand IDXCD
InChIInChI=1S/C21H19F3N4O2/c1-10-6-17(28-30-10)12(3)27-20(29)19-11(2)15(8-26-19)16-9-25-18-7-13(21(22,23)24)4-5-14(16)18/h4-9,12,25-26H,1-3H3,(H,27,29)/t12-/m1/s1
InChIKeyKJKYDILZECXCBA-GFCCVEGCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](NC(=O)c1[nH]cc(c1C)c2c[nH]c3cc(ccc23)C(F)(F)F)c4cc(C)on4
OpenEye OEToolkits 2.0.7Cc1cc(no1)C(C)NC(=O)c2c(c(c[nH]2)c3c[nH]c4c3ccc(c4)C(F)(F)F)C
OpenEye OEToolkits 2.0.7Cc1cc(no1)[C@@H](C)NC(=O)c2c(c(c[nH]2)c3c[nH]c4c3ccc(c4)C(F)(F)F)C
CACTVS 3.385C[C@@H](NC(=O)c1[nH]cc(c1C)c2c[nH]c3cc(ccc23)C(F)(F)F)c4cc(C)on4
ACDLabs 12.01Cc4cc(C(NC(c3c(c(c1c2c(nc1)cc(cc2)C(F)(F)F)cn3)C)=O)C)no4
FormulaC21 H19 F3 N4 O2
Name3-methyl-N-[(1R)-1-(5-methyl-1,2-oxazol-3-yl)ethyl]-4-[6-(trifluoromethyl)-1H-indol-3-yl]-1H-pyrrole-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7kyy Chain D Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7kyy Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F171 L172 G181 E182 C184 H185 F188 I263 R265 Y528 V532
Binding residue
(residue number reindexed from 1)		F11 L12 G21 E22 C24 H25 F28 I103 R105 Y333 V337
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G248 N274 F278 S345 N347 T348 K429 N458
Catalytic site (residue number reindexed from 1) G88 N114 F118 S185 N187 T188 K234 N263
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7kyy, PDBe:7kyy, PDBj:7kyy
PDBsum7kyy
PubMed33876936
UniProtQ08210|PYRD_PLAF7 Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=PFF0160c)

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