Structure of PDB 3wk3 Chain A Binding Site BS01

Receptor Information
>3wk3 Chain A (length=215) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFR
KRFGCRIIADFAVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESIKDL
Ligand information
Ligand IDO7E
InChIInChI=1S/C12H17N2O11P/c1-2-23-11(18)5-3-7(15)13-12(19)14(5)10-9(17)8(16)6(25-10)4-24-26(20,21)22/h3,6,8-10,16-17H,2,4H2,1H3,(H,13,15,19)(H2,20,21,22)/t6-,8-,9-,10-/m1/s1
InChIKeyDZWXMWNQARNSMH-PEBGCTIMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCOC(=O)C1=CC(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.385CCOC(=O)C1=CC(=O)NC(=O)N1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
CACTVS 3.385CCOC(=O)C1=CC(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.7.6CCOC(=O)C1=CC(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 12.01O=C(OCC)C=1N(C(=O)NC(=O)C=1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC12 H17 N2 O11 P
Name6-(ethoxycarbonyl)uridine 5'-(dihydrogen phosphate)
ChEMBL
DrugBank
ZINCZINC000098209257
PDB chain3wk3 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3wk3 Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.
Resolution1.26 Å
Binding residue
(original residue number in PDB)		D20 K42 D70 A72 L123 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D10 K32 D60 A62 L113 M116 S117 P170 Q175 G192 R193
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 A72 D75
Catalytic site (residue number reindexed from 1) K32 D60 A62 D65
Enzyme Commision number 4.1.1.23: orotidine-5'-phosphate decarboxylase.
Gene Ontology
Molecular Function
GO:0004590 orotidine-5'-phosphate decarboxylase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3wk3, PDBe:3wk3, PDBj:3wk3
PDBsum3wk3
PubMed24151964
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

[Back to BioLiP]