5NP8

PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation.

Bilsland, A.E.Liu, Y.Turnbull, A.Sumpton, D.Stevenson, K.Cairney, C.J.Boyd, S.M.Roffey, J.Jenkinson, D.Keith, W.N.

(2019) Neoplasia 21: 893-907

  • DOI: 10.1016/j.neo.2019.07.008
  • Primary Citation of Related Structures:  
    5NP8

  • PubMed Abstract: 
  • Telomere signaling and metabolic dysfunction are hallmarks of cell aging. New agents targeting these processes might provide therapeutic opportunities, including chemoprevention strategies against cancer predisposition. We report identification and characterization of a pyrazolopyrimidine compound series identified from screens focused on cell immortality and whose targets are glycolytic kinase PGK1 and oxidative stress sensor DJ1 ...

    Telomere signaling and metabolic dysfunction are hallmarks of cell aging. New agents targeting these processes might provide therapeutic opportunities, including chemoprevention strategies against cancer predisposition. We report identification and characterization of a pyrazolopyrimidine compound series identified from screens focused on cell immortality and whose targets are glycolytic kinase PGK1 and oxidative stress sensor DJ1. We performed structure-activity studies on the series to develop a photoaffinity probe to deconvolute the cellular targets. In vitro binding and structural analyses confirmed these targets, suggesting that PGK1/DJ1 interact, which we confirmed by immunoprecipitation. Glucose homeostasis and oxidative stress are linked to telomere signaling and exemplar compound CRT0063465 blocked hypoglycemic telomere shortening. Intriguingly, PGK1 and DJ1 bind to TRF2 and telomeric DNA. Compound treatment modulates these interactions and also affects Shelterin complex composition, while conferring cellular protection from cytotoxicity due to bleomycin and desferroxamine. These results demonstrate therapeutic potential of the compound series.


    Organizational Affiliation

    Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1QH, UK. Electronic address: nicol.keith@glasgow.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoglycerate kinase 1A420Homo sapiensMutation(s): 0 
Gene Names: PGK1PGKAMIG10OK/SW-cl.110
EC: 2.7.2.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00558 (Homo sapiens)
Explore P00558 
Go to UniProtKB:  P00558
PHAROS:  P00558
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
93T (Subject of Investigation/LOI)
Query on 93T

Download Ideal Coordinates CCD File 
B [auth A]3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid
C17 H16 Br N3 O2
SJELVUFWTXHLTJ-UHFFFAOYSA-N
 Ligand Interaction
3PG (Subject of Investigation/LOI)
Query on 3PG

Download Ideal Coordinates CCD File 
F [auth A]3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3PG BindingDB:  5NP8 Kd: 1.09e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.87α = 90
b = 103.9β = 99.1
c = 50.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references