Structure of PDB 7kyk Chain D Binding Site BS02

Receptor Information

>7kyk Chain D (length=369) Species: 36329 (Plasmodium falciparum 3D7)

NPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTN
IKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKP
RIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVS
IGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLK
NIILSVKEEIDNLEKNFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLL
ETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTN
KQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELN
HLLYQRGYYNLKEAIGRKH

Ligand information

• Ligand ID: FMN
• InChI: InChI=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
• InChIKey: FVTCRASFADXXNN-SCRDCRAPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
  ACDLabs 12.01: N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
• Formula: C17 H21 N4 O9 P
• Name: FLAVIN MONONUCLEOTIDE;
  RIBOFLAVIN MONOPHOSPHATE
• ChEMBL: CHEMBL1201794
• DrugBank: DB03247
• ZINC: ZINC000003831425
• PDB chain: 7kyk Chain D Residue 1002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7kyk Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series.
• Resolution: 2.15 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): A64 G65 T88 N113 N181 K232 S280 G281 S308 G309 G310 Y331 S332
• Annotation score: 1

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 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

External links

• PDB: RCSB:7kyk, PDBe:7kyk, PDBj:7kyk
• PDBsum: 7kyk
• PubMed: 33876936
• UniProt: Q08210|PYRD_PLAF7 Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=PFF0160c)