Structure of PDB 1dbt Chain B Binding Site BS01

Receptor Information
>1dbt Chain B (length=234) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNLPIIALDFASAEETLAFLAPFQQEPLFVKVGMELFYQEGPSIVKQLKE
RNCELFLDLKLHDIPTTVNKAMKRLASLGVDLVNVHAAGGKKMMQAALEG
LEEGTPAGKKRPSLIAVTQLTSTSEQIMKDELLIEKSLIDTVVHYSKQAE
ESGLDGVVCSVHEAKAIYQAVSPSFLTVTPGIRMSEDAANDQVRVATPAI
AREKGSSAIVVGRSITKAEDPVKAYKAVRLEWEG
Ligand information
Ligand IDU5P
InChIInChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyDJJCXFVJDGTHFX-XVFCMESISA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
NameURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL214393
DrugBankDB03685
ZINCZINC000002123545
PDB chain1dbt Chain A Residue 250 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1dbt The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D65 I66 T69
Binding residue
(residue number reindexed from 1)		D63 I64 T67
Annotation score3
Binding affinityMOAD: Ki=0.46mM
Enzymatic activity
Catalytic site (original residue number in PDB) K33 D60 K62 D65 T123 R215
Catalytic site (residue number reindexed from 1) K31 D58 K60 D63 T121 R213
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1dbt, PDBe:1dbt, PDBj:1dbt
PDBsum1dbt
PubMed10681442
UniProtP25971|PYRF_BACSU Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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