4ZCW

Structure of Human Enolase 2 in complex with SF2312


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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This is version 1.5 of the entry. See complete history


Literature

SF2312 is a natural phosphonate inhibitor of enolase.

Leonard, P.G.Satani, N.Maxwell, D.Lin, Y.H.Hammoudi, N.Peng, Z.Pisaneschi, F.Link, T.M.Lee, G.R.Sun, D.Prasad, B.A.Di Francesco, M.E.Czako, B.Asara, J.M.Wang, Y.A.Bornmann, W.DePinho, R.A.Muller, F.L.

(2016) Nat Chem Biol 12: 1053-1058

  • DOI: https://doi.org/10.1038/nchembio.2195
  • Primary Citation of Related Structures:  
    4ZA0, 4ZCW

  • PubMed Abstract: 

    Despite being crucial for energy generation in most forms of life, few if any microbial antibiotics specifically inhibit glycolysis. To develop a specific inhibitor of the glycolytic enzyme enolase 2 (ENO2) for the treatment of cancers with deletion of ENO1 (encoding enolase 1), we modeled the synthetic tool compound inhibitor phosphonoacetohydroxamate (PhAH) into the active site of human ENO2. A ring-stabilized analog of PhAH, in which the hydroxamic nitrogen is linked to Cα by an ethylene bridge, was predicted to increase binding affinity by stabilizing the inhibitor in a bound conformation. Unexpectedly, a structure-based search revealed that our hypothesized backbone-stabilized PhAH bears strong similarity to SF2312, a phosphonate antibiotic of unknown mode of action produced by the actinomycete Micromonospora, which is active under anaerobic conditions. Here, we present multiple lines of evidence, including a novel X-ray structure, that SF2312 is a highly potent, low-nanomolar inhibitor of enolase.


  • Organizational Affiliation

    Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX 77054.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-enolase
A, B
440Homo sapiensMutation(s): 0 
Gene Names: ENO2
EC: 4.2.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P09104 (Homo sapiens)
Explore P09104 
Go to UniProtKB:  P09104
PHAROS:  P09104
GTEx:  ENSG00000111674 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09104
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.3α = 90
b = 109.46β = 90
c = 117.27γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-10-05
    Changes: Database references
  • Version 1.2: 2016-10-26
    Changes: Database references
  • Version 1.3: 2016-11-23
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Refinement description
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description