Structure of PDB 5c3s Chain B Binding Site BS02

Receptor Information

>5c3s Chain B (length=310) Species: 5141 (Neurospora crassa)

MEKAAVNEDGLVIPLIDFSKFLEGDETLKLETAKAILHGFQTAGFIYLKN
IPIQPDFREHVFNTSAKFFKLPKEKKLEVGWTTPEANRGYSAPDIKESYE
IGREDEPGHPNPWPAEQDDLVGFKSTMNNFFDQCKALHIEVMRAIAVGMG
IDANYFDSFVDVGDNILRLLHYPAVKSEVFKINPGQVRAGEHTDYGSITL
LFQDSRGGLQVKSPNGQFIDATPIENTVVVNAGDLLARWSNDTIKSTVHR
VVEPPKQEDVHPPRYSIAYFCNPNHKSYIEAIPGTYAAESERKYEGINSG
KYLVQRLAAT

Ligand information

• Ligand ID: FYU
• InChI: InChI=1S/C5H4N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1-2H,(H2,6,7,9,10)
• InChIKey: OHAMXGZMZZWRCA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: N1C(NC(C(=C1)C=O)=O)=O
  CACTVS 3.385: O=CC1=CNC(=O)NC1=O
  OpenEye OEToolkits 1.9.2: C1=C(C(=O)NC(=O)N1)C=O
• Formula: C5 H4 N2 O3
• Name: 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbaldehyde;
  5-formyluracil
• ZINC: ZINC000000434270
• PDB chain: 5c3s Chain B Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5c3s Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): R190 D216 Y217 F292
• Binding residue (residue number reindexed from 1): R168 D194 Y195 F270
• Annotation score: 1
• Binding affinity: MOAD: Kd=108uM

Enzymatic activity

• Catalytic site (original residue number in PDB): R190 A211 H214 D216 H271
• Catalytic site (residue number reindexed from 1): R168 A189 H192 D194 H249

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0044283 small molecule biosynthetic process

External links

• PDB: RCSB:5c3s, PDBe:5c3s, PDBj:5c3s
• PDBsum: 5c3s
• PubMed: 26429971
• UniProt: Q7RYZ9