Structure of PDB 2e6d Chain A Binding Site BS01

Receptor Information

>2e6d Chain A (length=312) Species: 5693 (Trypanosoma cruzi)

MCLKLNLLDHVFANPFMNAAGVLCSTEEDLRCMTASSSGALVSKSCTSAP
RDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSIS
GLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTY
LQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNG
LVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCG
GVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYR
TLEEFRGRVKTI

Ligand information

• Ligand ID: FMN
• InChI: InChI=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
• InChIKey: FVTCRASFADXXNN-SCRDCRAPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
  ACDLabs 12.01: N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
• Formula: C17 H21 N4 O9 P
• Name: FLAVIN MONONUCLEOTIDE;
  RIBOFLAVIN MONOPHOSPHATE
• ChEMBL: CHEMBL1201794
• DrugBank: DB03247
• ZINC: ZINC000003831425
• PDB chain: 2e6d Chain A Residue 1350

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2e6d Structures of Trypanosoma cruzi dihydroorotate dehydrogenase complexed with substrates and products: atomic resolution insights into mechanisms of dihydroorotate oxidation and fumarate reduction
• Resolution: 1.94 Å
• Binding residue (original residue number in PDB): A18 A19 G20 K43 S44 M69 N127 K164 N194 G221 G222 I225 C248 G249 G250 G271 T272
• Binding residue (residue number reindexed from 1): A19 A20 G21 K44 S45 M70 N128 K165 N195 G222 G223 I226 C249 G250 G251 G272 T273
• Annotation score: 1

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

External links

• PDB: RCSB:2e6d, PDBe:2e6d, PDBj:2e6d
• PDBsum: 2e6d
• PubMed: 18808149
• UniProt: Q4D3W2|PYRD_TRYCC Dihydroorotate dehydrogenase (fumarate) (Gene Name=pyr4)