Structure of PDB 5del Chain A Binding Site BS02

Receptor Information
>5del Chain A (length=374) 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
IKRELNHLLYQRGYYNLKEAIGRK
Ligand information
Ligand IDD59
InChIInChI=1S/C14H10Cl2N2O3/c1-8-12(3-2-4-13(8)18(20)21)14(19)17-11-6-9(15)5-10(16)7-11/h2-7H,1H3,(H,17,19)
InChIKeyNKIJNFMSYDSAJK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1c(cccc1[N+]([O-])=O)C(=O)Nc2cc(Cl)cc(Cl)c2
ACDLabs 12.01Clc2cc(NC(=O)c1cccc([N+]([O-])=O)c1C)cc(Cl)c2
OpenEye OEToolkits 1.7.6Cc1c(cccc1[N+](=O)[O-])C(=O)Nc2cc(cc(c2)Cl)Cl
FormulaC14 H10 Cl2 N2 O3
NameN-(3,5-dichlorophenyl)-2-methyl-3-nitrobenzamide
ChEMBLCHEMBL217893
DrugBank
ZINCZINC000000304714
PDB chain5del Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5del The X-ray structure of Plasmodium falciparum dihydroorotate dehydrogenase bound to a potent and selective N-phenylbenzamide inhibitor reveals novel binding-site interactions.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G181 H185 F188 F227 I263 R265 Y528 L531 V532 G535 M536
Binding residue
(residue number reindexed from 1)		G20 H24 F27 F66 I102 R104 Y337 L340 V341 G344 M345
Annotation score1
Binding affinityMOAD: ic50=16nM
BindingDB: IC50=151nM,Ki=30nM
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:5del, PDBe:5del, PDBj:5del
PDBsum5del
PubMed25945708
UniProtQ08210|PYRD_PLAF7 Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=PFF0160c)

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