› 4jzr

X-ray diffraction
2.1Å resolution

Structure of Prolyl Hydroxylase Domain-containing Protein (PHD) with Inhibitors

Released:
DOI: 10.2210/pdb4jzr/pdb
PDB entry 4jzr coloured by chain, front view.
PDB entry 4jzr coloured by chain, side view.
PDB entry 4jzr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Novel complex crystal structure of prolyl hydroxylase domain-containing protein 2 (PHD2): 2,8-Diazaspiro[4.5]decan-1-ones as potent, orally bioavailable PHD2 inhibitors.
Deng G, Zhao B, Ma Y, Xu Q, Wang H, Yang L, Zhang Q, Guo TB, Zhang W, Jiao Y, Cai X, Zhang J, Liu H, Guan X, Lu H, Xiang J, Elliott JD, Lin X, Ren F
Bioorg Med Chem 21 6349-58 (2013)
PMID: 24055079

Function and Biology Details

Reaction catalysed: 
Hypoxia-inducible factor-L-proline + 2-oxoglutarate + O(2) = hypoxia-inducible factor-trans-4-hydroxy-L-proline + succinate + CO(2)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190450 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Egl nine homolog 1 Chain: A
Molecule details ›
Chain: A
Length: 216 amino acids
Theoretical weight: 24.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9GZT9 (Residues: 189-399; Coverage: 50%)
Gene names: C1orf12, EGLN1, PNAS-118, PNAS-137
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: q2cbj1_9rhob like domain

Ligands and Environments

3 bound ligands:
Ligand NI 1 x NI
Ligand 4JR 1 x 4JR
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P63
Unit cell:
a: 111.455Å b: 111.455Å c: 39.974Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.232 0.231 0.259
Expression system: Escherichia coli

Quick links

Citations

1 review citation

π-Cation Interactions in Molecular Recognition: Perspectives on Pharmaceuticals and Pesticides.
Liang et al. (2018)
3 other articles

2 mentions without citation

Studies on spiro[4.5]decanone prolyl hydroxylase domain inhibitors.
Holt-Martyn et al. (2019)
1 more