2VF3

Aquifex aeolicus IspE in complex with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibitors of the Kinase Ispe: Structure-Activity Relationships and Co-Crystal Structure Analysis.

Hirsch, A.K.Alphey, M.S.Lauw, S.Seet, M.Barandun, L.Eisenreich, W.Rohdich, F.Hunter, W.N.Bacher, A.Diederich, F.

(2008) Org.Biomol.Chem. 6: 2719

  • DOI: 10.1039/b804375b

  • PubMed Abstract: 
  • Enzymes of the non-mevalonate pathway for isoprenoid biosynthesis are therapeutic targets for the treatment of important infectious diseases. Whereas this pathway is absent in humans, it is used by plants, many eubacteria and apicomplexan protozoa, i ...

    Enzymes of the non-mevalonate pathway for isoprenoid biosynthesis are therapeutic targets for the treatment of important infectious diseases. Whereas this pathway is absent in humans, it is used by plants, many eubacteria and apicomplexan protozoa, including major human pathogens such as Plasmodium falciparum and Mycobacterium tuberculosis. Herein, we report on the design, preparation and biological evaluation of a new series of ligands for IspE protein, a kinase from this pathway. These inhibitors were developed for the inhibition of IspE from Escherichia coli, using structure-based design approaches. Structure-activity relationships (SARs) and a co-crystal structure of Aquifex aeolicus IspE bound to a representative inhibitor validate the proposed binding mode. The crystal structure shows that the ligand binds in the substrate-rather than the adenosine 5'-triphosphate (ATP)-binding pocket. As predicted, a cyclopropyl substituent occupies a small cavity not used by the substrate. The optimal volume occupancy of this cavity is explored in detail. In the co-crystal structure, a diphosphate anion binds to the Gly-rich loop, which normally accepts the triphosphate moiety of ATP. This structure provides useful insights for future structure-based developments of inhibitors for the parasite enzymes.


    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
GVS
Query on GVS

Download SDF File 
Download CCD File 
A, B
ethyl {3-[4-amino-5-{3-[(cyclopropylsulfonyl)amino]prop-1-yn-1-yl}-2-oxopyrimidin-1(2H)-yl]oxetan-3-yl}acetate
C17 H22 N4 O6 S
MIAWQMZUJQYSPX-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

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Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BR
Query on BR

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Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 137.318α = 90.00
b = 137.318β = 90.00
c = 137.318γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance