› 6wl6

X-ray diffraction
2.12Å resolution

Cocomplex structure of Deoxyhypusine synthase with inhibitor 6-[(2R)-1-AMINO-4-METHYLPENTAN-2-YL]-3-(PYRIDIN-3-YL)-4H,5H,6H,7H-THIENO[2,3-C]PYRIDIN-7-ONE

Released:
DOI: 10.2210/pdb6wl6/pdb
PDB entry 6wl6 coloured by chain, front view.
PDB entry 6wl6 coloured by chain, side view.
PDB entry 6wl6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
New Series of Potent Allosteric Inhibitors of Deoxyhypusine Synthase.
Tanaka Y, Kurasawa O, Yokota A, Klein MG, Saito B, Matsumoto S, Okaniwa M, Ambrus-Aikelin G, Uchiyama N, Morishita D, Kimura H, Imamura S
ACS Med Chem Lett 11 1645-1652 (2020)
PMID: 34345355

Function and Biology Details

Reaction catalysed: 
(1a) spermidine + NAD(+) = dehydrospermidine + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155939 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyhypusine synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 372 amino acids
Theoretical weight: 41.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49366 (Residues: 1-369; Coverage: 100%)
Gene names: DHPS, DS
Sequence domains: Deoxyhypusine synthase

Ligands and Environments

1 bound ligand:
Ligand 91A 2 x 91A
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: P3221
Unit cell:
a: 105.988Å b: 105.988Å c: 157.068Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.179 0.194
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Translation factor accelerating peptide bond formation on the ribosome: EF-P and eIF5A as entropic catalysts and a potential drug targets.
Mudryi et al. (2023)
1 more

1 mention without citation

New Series of Potent Allosteric Inhibitors of Deoxyhypusine Synthase.
Tanaka et al. (2020)