Structure of PDB 3kvj Chain A Binding Site BS01

Receptor Information
>3kvj Chain A (length=363) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDERFYAHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRV
LGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPR
VFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLG
KNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRL
LTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVT
NTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGV
GGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGF
GGVTDAIGADHRR
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 chain3kvj Chain A Residue 398 [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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PDB3kvj Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		A96 G97 K100 S120 N145 N181 N212 K255 N284 S305 G306 V333 G334 G335 L355 Y356 T357
Binding residue
(residue number reindexed from 1)		A63 G64 K67 S87 N112 N148 N179 K222 N251 S272 G273 V300 G301 G302 L322 Y323 T324
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G119 N145 F149 S215 N217 T218 K255 N284
Catalytic site (residue number reindexed from 1) G86 N112 F116 S182 N184 T185 K222 N251
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3kvj, PDBe:3kvj, PDBj:3kvj
PDBsum3kvj
PubMed20153645
UniProtQ02127|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

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