Crystal structure of 6-phosphogluconate dehydrogenase complexed with 3-phosphoglyceric acid

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth.

Hitosugi, T.Zhou, L.Elf, S.Fan, J.Kang, H.B.Seo, J.H.Shan, C.Dai, Q.Zhang, L.Xie, J.Gu, T.L.Jin, P.Aleckovic, M.Leroy, G.Kang, Y.Sudderth, J.A.Deberardinis, R.J.Luan, C.H.Chen, G.Z.Muller, S.Shin, D.M.Owonikoko, T.K.Lonial, S.Arellano, M.L.Khoury, H.J.Khuri, F.R.Lee, B.H.Ye, K.Boggon, T.J.Kang, S.He, C.Chen, J.

(2012) Cancer Cell 22: 585-600

  • DOI: https://doi.org/10.1016/j.ccr.2012.09.020
  • Primary Citation of Related Structures:  
    4GWG, 4GWK

  • PubMed Abstract: 

    It is unclear how cancer cells coordinate glycolysis and biosynthesis to support rapidly growing tumors. We found that the glycolytic enzyme phosphoglycerate mutase 1 (PGAM1), commonly upregulated in human cancers due to loss of TP53, contributes to biosynthesis regulation in part by controlling intracellular levels of its substrate, 3-phosphoglycerate (3-PG), and product, 2-phosphoglycerate (2-PG). 3-PG binds to and inhibits 6-phosphogluconate dehydrogenase in the oxidative pentose phosphate pathway (PPP), while 2-PG activates 3-phosphoglycerate dehydrogenase to provide feedback control of 3-PG levels. Inhibition of PGAM1 by shRNA or a small molecule inhibitor PGMI-004A results in increased 3-PG and decreased 2-PG levels in cancer cells, leading to significantly decreased glycolysis, PPP flux and biosynthesis, as well as attenuated cell proliferation and tumor growth.

  • Organizational Affiliation

    Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase, decarboxylating484Homo sapiensMutation(s): 0 
Gene Names: PGDPGDH
UniProt & NIH Common Fund Data Resources
Find proteins for P52209 (Homo sapiens)
Explore P52209 
Go to UniProtKB:  P52209
GTEx:  ENSG00000142657 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52209
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
3PG PDBBind:  4GWK Kd: 4.60e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.246α = 90
b = 87.246β = 90
c = 130.424γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description