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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1-deoxy-D-xylulose 5-phosphate reductoisomeraseA, B410Escherichia coli K-12Mutation(s): 0 
Gene Names: dxrispCyaeMb0173JW0168
EC: 1.1.1.267
Find proteins for P45568 (Escherichia coli (strain K12))
Explore P45568 
Go to UniProtKB:  P45568
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C0K
Query on C0K

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]{(1S)-1-(3,4-difluorophenyl)-4-[hydroxy(methyl)amino]-4-oxobutyl}phosphonic acid
C11 H14 F2 N O5 P
IZWIBRNXHRUNKD-JTQLQIEISA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C0KIC50 :  120   nM  PDBBind
C0KIC50:  120   nM  Binding MOAD
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

View Full Validation Report



Entry History 

Deposition Data

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