5N53

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    5OFW, 5OFV, 5NZQ, 5NZP, 5NZO, 5N53

  • 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

    Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-3-phosphoglycerate dehydrogenaseAB195Homo sapiensMutation(s): 0 
Gene Names: PHGDHPGDH3
EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (UniProt), 1.1.1.37 (UniProt)
Find proteins for O43175 (Homo sapiens)
Explore O43175 
Go to UniProtKB:  O43175
NIH Common Fund Data Resources
PHAROS  O43175
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8NB
Query on 8NB

Download CCD File 
A, B
~{N}-(3-chloranyl-4-methoxy-phenyl)ethanamide
C9 H10 Cl N O2
WNOVNNUWOUKIOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8NBKd:  2800000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.353α = 97.9
b = 45.323β = 110.06
c = 55.255γ = 106.35
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC2115/A21421

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references