Structure of PDB 3i65 Chain A Binding Site BS01

Receptor Information
>3i65 Chain A (length=370) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYAC
TNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNA
KPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVG
VSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNEAGKLKNIILSV
KEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLL
ETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTN
KQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELN
HLLYQRGYYNLKEAIGRKHS
Ligand information
Ligand IDJZ8
InChIInChI=1S/C16H13N5/c1-11-8-15(21-16(19-11)17-10-18-21)20-14-7-6-12-4-2-3-5-13(12)9-14/h2-10H,1H3,(H,17,18,19,20)/p+2
InChIKeyGNJXIZOPHGMAQW-UHFFFAOYSA-P
SMILES
SoftwareSMILES
ACDLabs 11.02n1c(cc([n+]2c1[nH+]cn2)Nc4cc3ccccc3cc4)C
OpenEye OEToolkits 1.7.0Cc1cc([n+]2c(n1)[nH+]c[nH]2)Nc3ccc4ccccc4c3
CACTVS 3.352Cc1cc(Nc2ccc3ccccc3c2)[n+]4[nH]c[nH+]c4n1
FormulaC16 H15 N5
Name5-methyl-7-(naphthalen-2-ylamino)-1H-[1,2,4]triazolo[1,5-a]pyrimidine-3,8-diium
ChEMBL
DrugBank
ZINC
PDB chain3i65 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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PDB3i65 Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G181 C184 H185 F188 L189 F227 R265 L531 V532 M536
Binding residue
(residue number reindexed from 1)		G22 C25 H26 F29 L30 F68 R106 L334 V335 M339
Annotation score1
Binding affinityMOAD: ic50=0.047uM
Enzymatic activity
Catalytic site (original residue number in PDB) G248 N274 F278 S345 N347 K429 N458
Catalytic site (residue number reindexed from 1) G89 N115 F119 S186 N188 K232 N261
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
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Cellular Component
External links
PDB RCSB:3i65, PDBe:3i65, PDBj:3i65
PDBsum3i65
PubMed19640844
UniProtQ08210|PYRD_PLAF7 Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=PFF0160c)

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