Structure of PDB 6fmd Chain A Binding Site BS01

Receptor Information
>6fmd Chain A (length=357) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLE
VRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNP
RPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGV
NLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPGKAELRRLLTKVLQ
ERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSR
PAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSG
QDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDA
IGADHRR
Ligand information
Ligand IDDUH
InChIInChI=1S/C20H11F4N3O2/c21-14-12(10-6-2-1-3-7-10)15(22)17(24)18(16(14)23)25-19(28)13-11-8-4-5-9-27(11)26-20(13)29/h1-9H,(H,25,28)(H,26,29)
InChIKeyJIIXZPWFDKPNKW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Oc1nn2ccccc2c1C(=O)Nc3c(F)c(F)c(c(F)c3F)c4ccccc4
OpenEye OEToolkits 2.0.6c1ccc(cc1)c2c(c(c(c(c2F)F)NC(=O)c3c4ccccn4nc3O)F)F
FormulaC20 H11 F4 N3 O2
Name2-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]pyrazolo[1,5-a]pyridine-3-carboxamide
ChEMBLCHEMBL4173846
DrugBank
ZINC
PDB chain6fmd Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fmd Targeting Myeloid Differentiation Using Potent 2-Hydroxypyrazolo[1,5- a]pyridine Scaffold-Based Human Dihydroorotate Dehydrogenase Inhibitors.
Resolution1.58 Å
Binding residue
(original residue number in PDB)		M43 Q47 P52 A55 H56 A59 V134 R136 Y356 T360 P364
Binding residue
(residue number reindexed from 1)		M13 Q17 P22 A25 H26 A29 V104 R106 Y317 T321 P325
Annotation score1
Binding affinityMOAD: ic50=0.0012uM
BindingDB: IC50=1.2nM
Enzymatic activity
Catalytic site (original residue number in PDB) G119 N145 F149 S215 K255 N284
Catalytic site (residue number reindexed from 1) G89 N115 F119 S185 K216 N245
Enzyme Commision number 1.3.5.2: dihydroorotate dehydrogenase (quinone).
Gene Ontology
Molecular Function
GO:0004151 dihydroorotase activity
GO:0004152 dihydroorotate dehydrogenase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0106430 dihydroorotate dehydrogenase (quinone) activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0009220 pyrimidine ribonucleotide biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005829 cytosol
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:6fmd, PDBe:6fmd, PDBj:6fmd
PDBsum6fmd
PubMed29939742
UniProtQ02127|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

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