4ZA0

Structure of Human Enolase 2 in complex with Phosphonoacetohydroxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1038/nchembio.2195
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-enolase
A, B
440Homo sapiensMutation(s): 0 
Gene Names: ENO2
EC: 4.2.1.11
Find proteins for P09104 (Homo sapiens)
Go to Gene View: ENO2
Go to UniProtKB:  P09104
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PAH
Query on PAH

Download SDF File 
Download CCD File 
A, B
PHOSPHONOACETOHYDROXAMIC ACID
C2 H6 N O5 P
LDKRAXXVBWHMRH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PAHIC50: 62.3 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.790α = 90.00
b = 108.671β = 90.00
c = 112.210γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
iMOSFLMdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references
  • Version 1.2: 2016-10-26
    Type: Database references
  • Version 1.3: 2016-11-23
    Type: Database references
  • Version 1.4: 2017-11-22
    Type: Refinement description