Structure of PDB 4lc8 Chain A Binding Site BS01

Receptor Information
>4lc8 Chain A (length=222) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDII
AEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSV
RACLNVAEEMGREVFLLTEMSNPGAEMFIQGAADEIARMGVDLGVKNYVG
PSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIY
LADNPAAAAAGIIESIKDLLNP
Ligand information
Ligand IDBMP
InChIInChI=1S/C9H13N2O10P/c12-4-1-5(13)11(9(16)10-4)8-7(15)6(14)3(21-8)2-20-22(17,18)19/h1,3,6-8,13-15H,2H2,(H,10,12,16)(H2,17,18,19)/t3-,6-,7-,8-/m1/s1
InChIKeyUDOBICLZEKUKCV-YXZULKJRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2O
ACDLabs 10.04O=C1NC(=O)N(C(O)=C1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H13 N2 O10 P
Name6-HYDROXYURIDINE-5'-PHOSPHATE
ChEMBLCHEMBL383923
DrugBankDB02890
ZINCZINC000024479522
PDB chain4lc8 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

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PDB4lc8 Crystal structure of the mutant H128N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP
Resolution1.318 Å
Binding residue
(original residue number in PDB)		D20 K72 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D14 K66 M120 S121 P174 Q179 G196 R197
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K36 D64 K66 D69
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:4lc8, PDBe:4lc8, PDBj:4lc8
PDBsum4lc8
PubMed
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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