4KP7

Structure of Plasmodium IspC in complex with a beta-thia-isostere derivative of Fosmidomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

IspC as Target for Antiinfective Drug Discovery: Synthesis, Enantiomeric Separation, and Structural Biology of Fosmidomycin Thia Isosters.

Kunfermann, A.Lienau, C.Illarionov, B.Held, J.Grawert, T.Behrendt, C.T.Werner, P.Hahn, S.Eisenreich, W.Riederer, U.Mordmuller, B.Bacher, A.Fischer, M.Groll, M.Kurz, T.

(2013) J.Med.Chem. 56: 8151-8162

  • DOI: 10.1021/jm4012559

  • PubMed Abstract: 
  • The emergence and spread of multidrug-resistant pathogens are widely believed to endanger human health. New drug targets and lead compounds exempt from cross-resistance with existing drugs are urgently needed. We report on the synthesis and propertie ...

    The emergence and spread of multidrug-resistant pathogens are widely believed to endanger human health. New drug targets and lead compounds exempt from cross-resistance with existing drugs are urgently needed. We report on the synthesis and properties of "reverse" thia analogs of fosmidomycin, which inhibit the first committed enzyme of a metabolic pathway that is essential for the causative agents of tuberculosis and malaria but is absent in the human host. Notably, IspC displays a high level of enantioselectivity for an α-substituted fosmidomycin derivative.


    Organizational Affiliation

    Center for Integrated Protein Science Munich, Lehrstuhl für Biochemie, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast
A, B
427Plasmodium falciparum (isolate HB3)Mutation(s): 0 
Gene Names: DXR
EC: 1.1.1.267
Find proteins for O96693 (Plasmodium falciparum (isolate HB3))
Go to UniProtKB:  O96693
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1UQ
Query on 1UQ

Download SDF File 
Download CCD File 
A, B
[(S)-({2-[hydroxy(methyl)amino]-2-oxoethyl}sulfanyl)(phenyl)methyl]phosphonic acid
C10 H14 N O5 P S
IWQBQVIYTMIQRL-JTQLQIEISA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
MN3
Query on MN3

Download SDF File 
Download CCD File 
A, B
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1UQIC50: 9.4 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.460α = 90.00
b = 78.120β = 91.53
c = 99.990γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references
  • Version 1.2: 2014-02-12
    Type: Database references