5NZQ

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-(1,3-oxazol-5-yl)aniline.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.

Unterlass, J.E.Basle, A.Blackburn, T.J.Tucker, J.Cano, C.Noble, M.E.M.Curtin, N.J.

(2018) Oncotarget 9: 13139-13153

  • DOI: 10.18632/oncotarget.11487
  • Primary Citation of Related Structures:  
  • Also Cited By: 5OFM

  • PubMed Abstract: 
  • 3-Phosphoglycerate dehydrogenase (PHGDH) has recently been identified as an attractive target in cancer therapy as it links upregulated glycolytic flux to increased biomass production in cancer cells. PHGDH catalyses the first step in the serine synt ...

    3-Phosphoglycerate dehydrogenase (PHGDH) has recently been identified as an attractive target in cancer therapy as it links upregulated glycolytic flux to increased biomass production in cancer cells. PHGDH catalyses the first step in the serine synthesis pathway and thus diverts glycolytic flux into serine synthesis. We have used siRNA-mediated suppression of PHGDH expression to show that PHGDH is a potential therapeutic target in PHGDH -amplified breast cancer. Knockdown caused reduced proliferation in the PHGDH -amplified cell line MDA-MB-468, whereas breast cancer cells with low PHGDH expression or with elevated PHGDH expression in the absence of genomic amplification were not affected. As a first step towards design of a chemical probe for PHGDH, we report a fragment-based drug discovery approach for the identification of PHGDH inhibitors. We designed a truncated PHGDH construct that gave crystals which diffracted to high resolution, and could be used for fragment soaking. 15 fragments stabilising PHGDH were identified using a thermal shift assay and validated by X-ray crystallography and ITC competition experiments to exhibit 1.5-26.2 mM affinity for PHGDH. A structure-guided fragment growing approach was applied to the PHGDH binders from the initial screen, yielding greater understanding of the binding site and suggesting routes to achieve higher affinity NAD-competitive inhibitors.


    Organizational Affiliation

    Institute of Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK.,Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-3-phosphoglycerate dehydrogenase
B, A
223Homo sapiensMutation(s): 0 
Gene Names: PHGDH (PGDH3)
EC: 1.1.1.95
Find proteins for O43175 (Homo sapiens)
Go to Gene View: PHGDH
Go to UniProtKB:  O43175
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5AO
Query on 5AO

Download SDF File 
Download CCD File 
A, B
3-(1,3-oxazol-5-yl)aniline
C9 H8 N2 O
AIELNJDAOGTASK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.228 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.335α = 97.85
b = 45.914β = 111.05
c = 56.203γ = 106.04
Software Package:
Software NamePurpose
PHASERphasing
xia2data reduction
xia2data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC2115/A21421

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence
  • Version 1.2: 2018-04-04
    Type: Data collection, Database references