Structure of PDB 3sw6 Chain A Binding Site BS01

Receptor Information
>3sw6 Chain A (length=214) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFR
KRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESIKD
Ligand information
Ligand ID5FU
InChIInChI=1S/C9H12FN2O9P/c10-3-1-12(9(16)11-7(3)15)8-6(14)5(13)4(21-8)2-20-22(17,18)19/h1,4-6,8,13-14H,2H2,(H,11,15,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1
InChIKeyRNBMPPYRHNWTMA-UAKXSSHOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)F
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)F
ACDLabs 10.04FC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(F)C(=O)NC2=O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(F)C(=O)NC2=O
FormulaC9 H12 F N2 O9 P
Name5-FLUORO-URIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL474163
DrugBank
ZINC
PDB chain3sw6 Chain A Residue 1000 [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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PDB3sw6 Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase covalently modified by 5-fluoro-6-azido-UMP
Resolution1.5 Å
Binding residue
(original residue number in PDB)		D20 K72 L123 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D10 K62 L113 M116 S117 P170 Q175 G192 R193
Annotation score3
Binding affinityBindingDB: Ki=645000nM
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K32 D60 K62 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3sw6, PDBe:3sw6, PDBj:3sw6
PDBsum3sw6
PubMed
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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