7POE

Phosphoglycolate Phosphatase with Inhibitor CP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Glycolytic flux control by drugging phosphoglycolate phosphatase.

Jeanclos, E.Schlotzer, J.Hadamek, K.Yuan-Chen, N.Alwahsh, M.Hollmann, R.Fratz, S.Yesilyurt-Gerhards, D.Frankenbach, T.Engelmann, D.Keller, A.Kaestner, A.Schmitz, W.Neuenschwander, M.Hergenroder, R.Sotriffer, C.von Kries, J.P.Schindelin, H.Gohla, A.

(2022) Nat Commun 13: 6845-6845

  • DOI: https://doi.org/10.1038/s41467-022-34228-2
  • Primary Citation of Related Structures:  
    7PO7, 7POE

  • PubMed Abstract: 

    Targeting the intrinsic metabolism of immune or tumor cells is a therapeutic strategy in autoimmunity, chronic inflammation or cancer. Metabolite repair enzymes may represent an alternative target class for selective metabolic inhibition, but pharmacological tools to test this concept are needed. Here, we demonstrate that phosphoglycolate phosphatase (PGP), a prototypical metabolite repair enzyme in glycolysis, is a pharmacologically actionable target. Using a combination of small molecule screening, protein crystallography, molecular dynamics simulations and NMR metabolomics, we discover and analyze a compound (CP1) that inhibits PGP with high selectivity and submicromolar potency. CP1 locks the phosphatase in a catalytically inactive conformation, dampens glycolytic flux, and phenocopies effects of cellular PGP-deficiency. This study provides key insights into effective and precise PGP targeting, at the same time validating an allosteric approach to control glycolysis that could advance discoveries of innovative therapeutic candidates.


  • Organizational Affiliation

    Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol-3-phosphate phosphatase
A, B
321Mus musculusMutation(s): 2 
Gene Names: Pgp
EC: 3.1.3.21 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt
Find proteins for Q8CHP8 (Mus musculus)
Explore Q8CHP8 
Go to UniProtKB:  Q8CHP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CHP8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7VK (Subject of Investigation/LOI)
Query on 7VK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B],
G [auth B]
2-[[4-[4-[(2-carboxyphenyl)carbamoyl]phenoxy]phenyl]carbonylamino]benzoic acid
C28 H20 N2 O7
UIRNMCRFFYWCBB-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
J [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.902α = 90
b = 105.902β = 90
c = 83.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-07-03
    Changes: Database references, Refinement description