Structure of PDB 4nt0 Chain B Binding Site BS01

Receptor Information
>4nt0 Chain B (length=213) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSRRVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSE
GMDIIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFP
GADSVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGV
KNYVGPSTRPERLSRLREIIGQDSFLISPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESIK
Ligand information
Ligand ID3DU
InChIInChI=1S/C10H14NO9P/c12-5-1-2-11(7(13)3-5)10-9(15)8(14)6(20-10)4-19-21(16,17)18/h1-3,6,8-10,12,14-15H,4H2,(H2,16,17,18)/t6-,8-,9-,10-/m1/s1
InChIKeyBMAAJONJGSMHCR-PEBGCTIMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)C=C(O)C=C1)C(O)C2O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)C=C1O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.385O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=CC2=O)O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)C=C1O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=CC2=O)O
FormulaC10 H14 N O9 P
Name4-hydroxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-2(1H)-one;
3-deazauridine 5'-monophosphate
ChEMBL
DrugBank
ZINCZINC000013517513
PDB chain4nt0 Chain B 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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PDB4nt0 Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 3-deazauridine 5'-monophosphate
Resolution1.769 Å
Binding residue
(original residue number in PDB)		D20 K72 M126 S127 P180 G202 R203
Binding residue
(residue number reindexed from 1)		D19 K71 M125 S126 P179 G192 R193
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K41 D69 K71 D74
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:4nt0, PDBe:4nt0, PDBj:4nt0
PDBsum4nt0
PubMed
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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