6WKZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

New Series of Potent Allosteric Inhibitors of Deoxyhypusine Synthase.

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

(2020) ACS Med Chem Lett 11: 1645-1652

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00331
  • Primary Citation of Related Structures:  
    6WKZ, 6WL6

  • PubMed Abstract: 

    Deoxyhypusine synthase (DHPS) is the primary enzyme responsible for the hypusine modification and, thereby, activation of the eukaryotic translation initiation factor 5A (eIF5A), which is key in regulating the protein translation processes associated with tumor proliferation. Although DHPS inhibitors could be a promising therapeutic option for treating cancer, only a few studies reported druglike compounds with this inhibition property. Thus, in this work, we designed and synthesized a new chemical series possessing fused ring scaffolds designed from high-throughput screening hit compounds, discovering a 5,6-dihydrothieno[2,3- c ]pyridine derivative ( 26d ) with potent inhibitory activity; furthermore, the X-ray crystallographic analysis of the DHPS complex with 26d demonstrated a distinct allosteric binding mode compared to a previously reported inhibitor. These findings could be significantly useful in the functional analysis of conformational changes in DHPS as well as the structure-based design of allosteric 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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8Y1 (Subject of Investigation/LOI)
Query on 8Y1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-[(1R)-2-amino-1-phenylethyl]-3-(pyridin-3-yl)-5,6-dihydrothieno[2,3-c]pyridin-7(4H)-one
C20 H19 N3 O S
XFQSGUURGVJNCH-SFHVURJKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.232α = 90
b = 106.232β = 90
c = 157.471γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description