3ELC

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy

Ramsden, N.L., Buetow, L., Dawson, A., Kemp, L.A., Ulaganathan, V., Brenk, R., Klebe, G., Hunter, W.N.

(2009) J.Med.Chem. 52: 2531-2542

  • DOI: 10.1021/jm801475n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The nonmevalonate route to isoprenoid biosynthesis is essential in Gram-negative bacteria and apicomplexan parasites. The enzymes of this pathway are absent from mammals, contributing to their appeal as chemotherapeutic targets. One enzyme, 2C-methyl ...

    The nonmevalonate route to isoprenoid biosynthesis is essential in Gram-negative bacteria and apicomplexan parasites. The enzymes of this pathway are absent from mammals, contributing to their appeal as chemotherapeutic targets. One enzyme, 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), has been validated as a target by genetic approaches in bacteria. Virtual screening against Escherichia coli IspF (EcIspF) was performed by combining a hierarchical filtering methodology with molecular docking. Docked compounds were inspected and 10 selected for experimental validation. A surface plasmon resonance assay was developed and two weak ligands identified. Crystal structures of EcIspF complexes were determined to support rational ligand development. Cytosine analogues and Zn(2+)-binding moieties were characterized. One of the putative Zn(2+)-binding compounds gave the lowest measured K(D) to date (1.92 +/- 0.18 muM). These data provide a framework for the development of IspF inhibitors to generate lead compounds of therapeutic potential against microbial pathogens.

    Organizational Affiliation: 

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C
165Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ispF (mecS, ygbB)
EC: 4.6.1.12
Find proteins for P62617 (Escherichia coli (strain K12))
Go to UniProtKB:  P62617
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F01
Query on F01
Download SDF File 
Download CCD File 
A, B, C
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-fluoro-pyrimidin-2-one
4-amino-5-fluoro-1-((2R,3S,4R,5R)-tetrahydro-3,4-dihydroxy-5-(hydroxymethyl)furan-2-yl)pyrimidin-2(1H)-one
C9 H12 F N3 O5
STRZQWQNZQMHQR-UAKXSSHOSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GPP
Query on GPP
Download SDF File 
Download CCD File 
C
GERANYL DIPHOSPHATE
C10 H20 O7 P2
GVVPGTZRZFNKDS-JXMROGBWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F01Kd: 2020000 nM (100) BINDINGDB
F01Kd: 2020000 nM BINDINGMOAD
F01Kd: 2020000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.676α = 90.00
b = 54.833β = 99.66
c = 88.506γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
CrystalCleardata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Advisory, Refinement description