Structure of PDB 3kvm Chain A Binding Site BS02

Receptor Information
>3kvm Chain A (length=366) 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
QGFGGVTDAIGADHRR
Ligand information
Ligand IDDOR
InChIInChI=1S/C5H6N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h2H,1H2,(H,9,10)(H2,6,7,8,11)/t2-/m0/s1
InChIKeyUFIVEPVSAGBUSI-REOHCLBHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1[C@H](NC(=O)NC1=O)C(=O)O
OpenEye OEToolkits 1.5.0C1C(NC(=O)NC1=O)C(=O)O
CACTVS 3.341OC(=O)[CH]1CC(=O)NC(=O)N1
CACTVS 3.341OC(=O)[C@@H]1CC(=O)NC(=O)N1
ACDLabs 10.04O=C(O)C1NC(=O)NC(=O)C1
FormulaC5 H6 N2 O4
Name(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID;
DIHYDROOROTIC ACID
ChEMBL
DrugBankDB02129
ZINCZINC000003869850
PDB chain3kvm Chain A Residue 399 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kvm Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N145 Y147 G148 F149 S215 N217 N284 T285
Binding residue
(residue number reindexed from 1)		N115 Y117 G118 F119 S185 N187 N254 T255
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) G119 N145 F149 S215 N217 T218 K255 N284
Catalytic site (residue number reindexed from 1) G89 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:3kvm, PDBe:3kvm, PDBj:3kvm
PDBsum3kvm
PubMed20153645
UniProtQ02127|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

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