3ELC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 

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:  
    3ELC, 3EOR, 3ERN, 3ESJ, 3FBA

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseABC165Escherichia coli K-12Mutation(s): 0 
Gene Names: ispFmecSygbBb2746JW2716
EC: 4.6.1.12
Find proteins for P62617 (Escherichia coli (strain K12))
Explore P62617 
Go to UniProtKB:  P62617
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GPP
Query on GPP

Download CCD File 
C
GERANYL DIPHOSPHATE
C10 H20 O7 P2
GVVPGTZRZFNKDS-JXMROGBWSA-N
 Ligand Interaction
F01
Query on F01

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
C9 H12 F N3 O5
STRZQWQNZQMHQR-UAKXSSHOSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F01Kd:  2020000   nM  Binding MOAD
F01Kd:  2020000   nM  BindingDB
F01Kd :  2020000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.676α = 90
b = 54.833β = 99.66
c = 88.506γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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