2V2V

IspE in complex with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and Characterization of Cytidine Derivatives that Inhibit the Kinase Ispe of the Non-Mevalonate Pathway for Isoprenoid Biosynthesis.

Crane, C.M.Hirsch, A.K.Alphey, M.S.Sgraja, T.Lauw, S.Illarionova, V.Rohdich, F.Eisenreich, W.Hunter, W.N.Bacher, A.Diederich, F.

(2008) Chemmedchem 3: 91

  • DOI: 10.1002/cmdc.200700208
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzymes of the non-mevalonate pathway for isoprenoid biosynthesis are attractive targets for the development of novel drugs against malaria and tuberculosis. This pathway is used exclusively by the corresponding pathogens, but not by humans. A se ...

    The enzymes of the non-mevalonate pathway for isoprenoid biosynthesis are attractive targets for the development of novel drugs against malaria and tuberculosis. This pathway is used exclusively by the corresponding pathogens, but not by humans. A series of water-soluble, cytidine-based inhibitors that were originally designed for the fourth enzyme in the pathway, IspD, were shown to inhibit the subsequent enzyme, the kinase IspE (from Escherichia coli). The binding mode of the inhibitors was verified by co-crystal structure analysis, using Aquifex aeolicus IspE. The crystal structures represent the first reported example of a co-crystal structure of IspE with a synthetic ligand and confirmed that ligand binding affinity originates mainly from the interactions of the nucleobase moiety in the cytidine binding pocket of the enzyme. In contrast, the appended benzimidazole moieties of the ligands adopt various orientations in the active site and establish only poor intermolecular contacts with the protein. Defined binding sites for sulfate ions and glycerol molecules, components in the crystallization buffer, near the well-conserved ATP-binding Gly-rich loop of IspE were observed. The crystal structures of A. aeolicus IspE nicely complement the one from E. coli IspE for use in structure-based design, namely by providing invaluable structural information for the design of inhibitors targeting IspE from Mycobacterium tuberculosis and Plasmodium falciparum. Similar to the enzymes from these pathogens, A. aeolicus IspE directs the OH group of a tyrosine residue into a pocket in the active site. In the E. coli enzyme, on the other hand, this pocket is lined by phenylalanine and has a more pronounced hydrophobic character.


    Organizational Affiliation

    Laboratorium für Organische Chemie, ETH Zürich, HCI, CH-8093 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE
A, B
271Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: ispE
EC: 2.7.1.148
Find proteins for O67060 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67060
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
V12
Query on V12

Download SDF File 
Download CCD File 
A, B
5'-[(1H-BENZIMIDAZOL-2-YLACETYL)AMINO]-5'-DEOXYCYTIDINE
C18 H20 N6 O5
MMCWRTZSCVUETH-GAEVZRCVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V12Ki: 85800 nM BINDINGMOAD
V12Ki: 85800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 137.256α = 90.00
b = 137.256β = 90.00
c = 137.256γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance