Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.19 kDa 
• Atom Count: 3355 
• Residue Count: 390 
• Unique protein chains: 1

5NZQ

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

• DOI: 10.2210/pdb5NZQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-14 Released: 2017-06-14 
• Deposition Author(s): Unterlass, J.E., Basle, A., Blackburn, T.J., Tucker, J., Cano, C., Noble, M.E.M., Curtin, N.J.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.293 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

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

• PubMed: 29568346 
• DOI: 10.18632/oncotarget.11487
• Primary Citation of Related Structures:  
  5N53, 5OFW, 5OFV, 5NZQ, 5NZP, 5NZO


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase	A, B	223	Homo sapiens	Mutation(s): 0  Gene Names: PHGDH, PGDH3 EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (PDB Primary Data), 1.1.1.37 (PDB Primary Data)
Find proteins for O43175 (Homo sapiens) Explore O43175  Go to UniProtKB:  O43175
NIH Common Fund Data Resources
PHAROS:  O43175 GTEx:  ENSG00000092621

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5AO	A, B	3-(1,3-oxazol-5-yl)aniline C9 H8 N2 O AIELNJDAOGTASK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.293 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.335	α = 97.85
b = 45.914	β = 111.05
c = 56.203	γ = 106.04

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-14 
• Released Date: 2017-06-14 
Deposition Author(s): Unterlass, J.E., Basle, A., Blackburn, T.J., Tucker, J., Cano, C., Noble, M.E.M., Curtin, N.J.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C2115/A21421

Revision History 

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