5TLZ

Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor naphthalene 2,6-bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Bisphosphonate Inhibitors of Mammalian Glycolytic Aldolase.

Heron, P.W.Abellan-Flos, M.Salmon, L.Sygusch, J.

(2018) J Med Chem 61: 10558-10572

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01000
  • Primary Citation of Related Structures:  
    5TLE, 5TLH, 5TLW, 5TLZ

  • PubMed Abstract: 

    The glycolytic enzyme aldolase is an emerging drug target in diseases such as cancer and protozoan infections which are dependent on a hyperglycolytic phenotype to synthesize adenosine 5'-triphosphate and metabolic precursors for biomass production. To date, structural information for the enzyme in complex with phosphate-derived inhibitors has been lacking. Thus, we determined the crystal structure of mammalian aldolase in complex with naphthalene 2,6-bisphosphate (1) that served as a template for the design of bisphosphonate-based inhibitors, namely, 2-phosphate-naphthalene 6-bisphosphonate (2), 2-naphthol 6-bisphosphonate (3), and 1-phosphate-benzene 4-bisphosphonate (4). All inhibitors targeted the active site, and the most promising lead, 2, exhibited slow-binding inhibition with an overall inhibition constant of ∼38 nM. Compound 2 inhibited proliferation of HeLa cancer cells, whereas HEK293 cells expressing a normal phenotype were not inhibited. The crystal structures delineated the essential features of high-affinity phosphate-derived inhibitors and provide a template for the development of inhibitors with prophylaxis potential.


  • Organizational Affiliation

    Département de Biochimie et Médecine Moléculaire , Université de Montréal , CP 6128, Succursale Centre-Ville, Montréal , Québec H3C 3J7 , Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose-bisphosphate aldolase A
A, B, C, D
363Oryctolagus cuniculusMutation(s): 0 
Gene Names: ALDOA
EC: 4.1.2.13
UniProt
Find proteins for P00883 (Oryctolagus cuniculus)
Explore P00883 
Go to UniProtKB:  P00883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00883
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.254α = 90
b = 103.638β = 98.67
c = 84.518γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2022-11-09
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description