6P4V

1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Novel Allosteric Inhibitors of Deoxyhypusine Synthase.

Tanaka, Y.Kurasawa, O.Yokota, A.Klein, M.G.Ono, K.Saito, B.Matsumoto, S.Okaniwa, M.Ambrus-Aikelin, G.Morishita, D.Kitazawa, S.Uchiyama, N.Ogawa, K.Kimura, H.Imamura, S.

(2020) J Med Chem 63: 3215-3226

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01979
  • Primary Citation of Related Structures:  
    6P4V, 6PGR

  • PubMed Abstract: 

    Deoxyhypusine synthase (DHPS) utilizes spermidine and NAD as cofactors to incorporate a hypusine modification into the eukaryotic translation initiation factor 5A (eIF5A). Hypusine is essential for eIF5A activation, which, in turn, plays a key role in regulating protein translation of selected mRNA that are associated with the synthesis of oncoproteins, thereby enhancing tumor cell proliferation. Therefore, inhibition of DHPS is a promising therapeutic option for the treatment of cancer. To discover novel lead compounds that target DHPS, we conducted synthetic studies with a hit obtained via high-throughput screening. Optimization of the ring structures of the amide compound ( 2 ) led to bromobenzothiophene ( 11g ) with potent inhibitory activity against DHPS. X-ray crystallographic analysis of 11g complexed with DHPS revealed a dramatic conformational change in DHPS, which suggests the presence of a novel allosteric site. These findings provide the basis for the development of novel therapy distinct from spermidine mimetic inhibitors.


  • Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyhypusine synthase
A, B
372Homo sapiensMutation(s): 0 
Gene Names: DHPSDS
EC: 2.5.1.46
UniProt & NIH Common Fund Data Resources
Find proteins for P49366 (Homo sapiens)
Explore P49366 
Go to UniProtKB:  P49366
PHAROS:  P49366
GTEx:  ENSG00000095059 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49366
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.466α = 90
b = 104.466β = 90
c = 159.49γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description