3R0I

IspC in complex with an N-methyl-substituted hydroxamic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Reverse Fosmidomycin Derivatives against the Antimalarial Drug Target IspC (Dxr).

Behrendt, C.T.Kunfermann, A.Illarionova, V.Matheeussen, A.Pein, M.K.Grawert, T.Kaiser, J.Bacher, A.Eisenreich, W.Illarionov, B.Fischer, M.Maes, L.Groll, M.Kurz, T.

(2011) J Med Chem 54: 6796-6802

  • DOI: https://doi.org/10.1021/jm200694q
  • Primary Citation of Related Structures:  
    3R0I

  • PubMed Abstract: 

    Reverse hydroxamate-based inhibitors of IspC, a key enzyme of the non-mevalonate pathway of isoprenoid biosynthesis and a validated antimalarial target, were synthesized and biologically evaluated. The binding mode of one derivative in complex with EcIspC and a divalent metal ion was clarified by X-ray analysis. Pilot experiments have demonstrated in vivo potential.


  • Organizational Affiliation

    Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B
410Escherichia coli K-12Mutation(s): 0 
Gene Names: dxrispCyaeMb0173JW0168
EC: 1.1.1.267
UniProt
Find proteins for P45568 (Escherichia coli (strain K12))
Explore P45568 
Go to UniProtKB:  P45568
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45568
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
C0K PDBBind:  3R0I IC50: 120 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.254α = 90
b = 54.584β = 93.17
c = 107.798γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description