Structure of PDB 7kyy Chain D Binding Site BS02

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 IDFMN
InChIInChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
InChIKeyFVTCRASFADXXNN-SCRDCRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
FormulaC17 H21 N4 O9 P
NameFLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE
ChEMBLCHEMBL1201794
DrugBankDB03247
ZINCZINC000003831425
PDB chain7kyy Chain D Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)		A225 G226 T249 N274 N342 K429 S477 G478 S505 G506 G507 Y528 S529
Binding residue
(residue number reindexed from 1)		A65 G66 T89 N114 N182 K234 S282 G283 S310 G311 G312 Y333 S334
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

View graph for
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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