IspE in complex with ligand

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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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: https://doi.org/10.1002/cmdc.200700208
  • Primary Citation of Related Structures:  
    2V2Q, 2V2V

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
271Aquifex aeolicusMutation(s): 0 
Find proteins for O67060 (Aquifex aeolicus (strain VF5))
Explore O67060 
Go to UniProtKB:  O67060
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67060
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NVG

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
C19 H22 N6 O5
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
R [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]
C3 H8 O3
Query on BR

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
K [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
NVG Binding MOAD:  2V2Q Ki: 7.12e+4 (nM) from 1 assay(s)
PDBBind:  2V2Q Ki: 7.12e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.038α = 90
b = 137.038β = 90
c = 137.038γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other