Structure of PDB 4jdb Chain B Binding Site BS01

Receptor Information
>4jdb Chain B (length=313) Species: 353153 (Trypanosoma cruzi strain CL Brener) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MCLKLNLLDHVFANPFMNAAGVLCSTEEDLRCMTASSSGALVSKSCTSAP
RDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSIS
GLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTY
LQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNG
LVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCG
GVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYR
TLEEFRGRVKTIE
Ligand information
Ligand IDJDB
InChIInChI=1S/C18H16N2O5/c1-25-13-6-5-11-4-2-10(8-12(11)9-13)3-7-14-15(17(22)23)19-18(24)20-16(14)21/h2,4-6,8-9H,3,7H2,1H3,(H,22,23)(H2,19,20,21,24)
InChIKeyBIZXBPHEWFJZCA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6COc1ccc2ccc(cc2c1)CCC3=C(NC(=O)NC3=O)C(=O)O
ACDLabs 12.01O=C1NC(C(=O)O)=C(C(=O)N1)CCc3cc2cc(OC)ccc2cc3
CACTVS 3.370COc1ccc2ccc(CCC3=C(NC(=O)NC3=O)C(O)=O)cc2c1
FormulaC18 H16 N2 O5
Name5-[2-(7-methoxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
ChEMBLCHEMBL3991216
DrugBank
ZINCZINC000098209040
PDB chain4jdb Chain B Residue 401 [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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PDB4jdb Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-005
Resolution1.82 Å
Binding residue
(original residue number in PDB)		N53 N67 M69 G70 L71 N194 S195
Binding residue
(residue number reindexed from 1)		N54 N68 M70 G71 L72 N195 S196
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K43 N67 L71 C130 N132 V133 K164 V193
Catalytic site (residue number reindexed from 1) K44 N68 L72 C131 N133 V134 K165 V194
Enzyme Commision number 1.3.98.1: dihydroorotate oxidase (fumarate).
Gene Ontology
Molecular Function
GO:0004152 dihydroorotate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:1990663 dihydroorotate dehydrogenase (fumarate) activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006222 UMP biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4jdb, PDBe:4jdb, PDBj:4jdb
PDBsum4jdb
PubMed
UniProtQ4D3W2|PYRD_TRYCC Dihydroorotate dehydrogenase (fumarate) (Gene Name=pyr4)

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