› 4m5l

X-ray diffraction
1.09Å resolution

The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase

Released:
DOI: 10.2210/pdb4m5l/pdb
PDB entry 4m5l coloured by chain, front view.
PDB entry 4m5l coloured by chain, side view.
PDB entry 4m5l coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Yun MK, Hoagland D, Kumar G, Waddell MB, Rock CO, Lee RE, White SW
Bioorg Med Chem 22 2157-65 (2014)
PMID: 24613625

Function and Biology Details

Reaction catalysed: 
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150686 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase Chain: A
Molecule details ›
Chain: A
Length: 162 amino acids
Theoretical weight: 18.38 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P26281 (Residues: 1-159; Coverage: 100%)
Gene names: JW0138, b0142, folK
Sequence domains: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK)
Structure domains: 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK

Ligands and Environments

4 bound ligands:
Ligand APC 1 x APC
Ligand CA 3 x CA
Ligand GOL 1 x GOL
Ligand YH4 1 x YH4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 35.903Å b: 57.991Å c: 38.643Å
α: 90° β: 115.49° γ: 90°
R-values:
R R work R free
0.173 0.173 0.186
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases.
Bertacine Dias et al. (2018)
7 other articles

1 mention without citation

The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Yun et al. (2014)