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

Experimental Data Snapshot

  • Resolution: 1.48 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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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: https://doi.org/10.18632/oncotarget.11487
  • Primary Citation of Related Structures:  
    5N53, 5NZO, 5NZP, 5NZQ, 5OFV, 5OFW

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-3-phosphoglycerate dehydrogenaseA [auth B],
B [auth A]
195Homo sapiensMutation(s): 0 
Gene Names: PHGDHPGDH3
UniProt & NIH Common Fund Data Resources
Find proteins for O43175 (Homo sapiens)
Explore O43175 
Go to UniProtKB:  O43175
PHAROS:  O43175
GTEx:  ENSG00000092621 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43175
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8NB

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
C9 H10 Cl N O2
Binding Affinity Annotations 
IDSourceBinding Affinity
8NB Binding MOAD:  5N53 Kd: 2.80e+6 (nM) from 1 assay(s)
BindingDB:  5N53 Kd: 2.80e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC2115/A21421

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description