3ERN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.1 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-d-erythritol-2,4-cyclodiphosphate synthase (IspF), has been validated as a target by genetic approaches in bacteria ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C, D, E, F
A, B, C, D, E, F
165Escherichia coli K-12Mutation(s): 0 
Gene Names: ispFmecSygbBb2746JW2716
EC: 4.6.1.12
UniProt
Find proteins for P62617 (Escherichia coli (strain K12))
Explore P62617 
Go to UniProtKB:  P62617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62617
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAR
Query on CAR

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B],
M [auth C],
O [auth D],
P [auth E]
CYTOSINE ARABINOSE-5'-PHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-CCXZUQQUSA-N
 Ligand Interaction
GPP
Query on GPP

Download Ideal Coordinates CCD File 
L [auth B],
S [auth F]
GERANYL DIPHOSPHATE
C10 H20 O7 P2
GVVPGTZRZFNKDS-JXMROGBWSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth B],
R [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth D],
Q [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CAR BindingDB:  3ERN Kd: 1.89e+7 (nM) from 1 assay(s)
Binding MOAD:  3ERN Kd: 1.89e+7 (nM) from 1 assay(s)
PDBBind:  3ERN Kd: 1.89e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.856α = 90
b = 54.236β = 94.99
c = 118.384γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance