Structure of PDB 6oc0 Chain A Binding Site BS02

Receptor Information
>6oc0 Chain A (length=365) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLE
VRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNP
RPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGV
NLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAEL
RRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGL
IVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPI
IGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKE
QGFGGVTDAIGADHR
Ligand information
Ligand IDM4J
InChIInChI=1S/C26H19F3N4O/c27-26(28,29)24-14-23(33(32-24)20-10-8-19(9-11-20)31-25(34)15-30)18-7-12-22-17(13-18)6-5-16-3-1-2-4-21(16)22/h1-14H,15,30H2,(H,31,34)
InChIKeyYULUCECVQOCQFQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCC(=O)Nc1ccc(cc1)n2nc(cc2c3ccc4c(ccc5ccccc45)c3)C(F)(F)F
ACDLabs 12.01c5cc4c3c(cc(c2n(c1ccc(NC(=O)CN)cc1)nc(C(F)(F)F)c2)cc3)ccc4cc5
OpenEye OEToolkits 2.0.7c1ccc2c(c1)ccc3c2ccc(c3)c4cc(nn4c5ccc(cc5)NC(=O)CN)C(F)(F)F
FormulaC26 H19 F3 N4 O
NameN-{4-[5-(phenanthren-2-yl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}glycinamide
ChEMBLCHEMBL1650595
DrugBank
ZINCZINC000003960083
PDB chain6oc0 Chain A Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6oc0 Metabolic Modifier Screen Reveals Secondary Targets of Protein Kinase Inhibitors within Nucleotide Metabolism.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		Y37 A58 F61 T62 L66 L67 R69 L358 P363
Binding residue
(residue number reindexed from 1)		Y8 A29 F32 T33 L37 L38 R40 L329 P334
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) N144 F148 S214 N216 T217 K254 N283
Catalytic site (residue number reindexed from 1) N115 F119 S185 N187 T188 K225 N254
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:6oc0, PDBe:6oc0, PDBj:6oc0
PDBsum6oc0
PubMed31734178
UniProtQ02127|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

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