Structure of PDB 3sec Chain A Binding Site BS01

Receptor Information

>3sec Chain A (length=214) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H)

VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFR
KRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESIKD

Ligand information

• Ligand ID: PFU
• InChI: InChI=1S/C9H14N3O9P/c10-9(16)4-6(14)3(11-12-4)8-7(15)5(13)2(21-8)1-20-22(17,18)19/h2,5,7-8,13-15H,1H2,(H2,10,16)(H,11,12)(H2,17,18,19)/t2-,5-,7-,8+/m1/s1
• InChIKey: CUHDHRMGDRLFLH-FLLFQEBCSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C(C1C(C(C(O1)c2c(c([nH]n2)C(=O)N)O)O)O)OP(=O)(O)O
  OpenEye OEToolkits 1.7.0: C([C@@H]1[C@H]([C@H]([C@@H](O1)c2c(c([nH]n2)C(=O)N)O)O)O)OP(=O)(O)O
  CACTVS 3.370: NC(=O)c1[nH]nc([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)c1O
  CACTVS 3.370: NC(=O)c1[nH]nc([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)c1O
  ACDLabs 12.01: O=C(N)c1c(O)c(nn1)C2OC(COP(=O)(O)O)C(O)C2O
• Formula: C9 H14 N3 O9 P
• Name: (1S)-1,4-anhydro-1-(5-carbamoyl-4-hydroxy-1H-pyrazol-3-yl)-5-O-phosphono-D-ribitol;
  Pyrazofurin Monophosphate
• ChEMBL: CHEMBL1164953
• ZINC: ZINC000049803241
• PDB chain: 3sec Chain A Residue 2000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3sec Structural determinants for the inhibitory ligands of orotidine-5'-monophosphate decarboxylase.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): D20 K42 K72 M126 S127 P180 Q185 G202 R203
• Binding residue (residue number reindexed from 1): D10 K32 K62 M116 S117 P170 Q175 G192 R193
• Annotation score: 1

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

External links

• PDB: RCSB:3sec, PDBe:3sec, PDBj:3sec
• PDBsum: 3sec
• UniProt: O26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)