› 6st3

X-ray diffraction
2.43Å resolution

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide

Released:
DOI: 10.2210/pdb6st3/pdb
PDB entry 6st3 coloured by chain, front view.
PDB entry 6st3 coloured by chain, side view.
PDB entry 6st3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Activity Relationship and Crystallographic Studies on 4-Hydroxypyrimidine HIF Prolyl Hydroxylase Domain Inhibitors.
Holt-Martyn JP, Chowdhury R, Tumber A, Yeh TL, Abboud MI, Lippl K, Lohans CT, Langley GW, Figg W, McDonough MA, Pugh CW, Ratcliffe PJ, Schofield CJ
OpenAccess logo ChemMedChem 15 270-273 (2020)
PMID: 31751494

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 233 amino acids
Theoretical weight: 26.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9GZT9 (Residues: 181-407; Coverage: 53%)
Gene names: C1orf12, EGLN1, PNAS-118, PNAS-137
Sequence domains: 2OG-Fe(II) oxygenase superfamily

Ligands and Environments

3 bound ligands:
Ligand LUW 2 x LUW
Ligand FMT 2 x FMT
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Unit cell:
a: 72.87Å b: 80.58Å c: 83.92Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.192 0.217
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 citation in other articles

Synthesis of Novel Pyridine-Carboxylates as Small-Molecule Inhibitors of Human Aspartate/Asparagine-β-Hydroxylase.
Brewitz et al. (2020)
9 more