3ANL

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with pyridin-2-ylmethylphosphonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase/Lipophilic Phosphonate Complexes

Deng, L.Endo, K.Kato, M.Cheng, G.Yajima, S.Song, Y.

(2011) ACS Med Chem Lett 2: 165-170

  • DOI: 10.1021/ml100243r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fosmidomycin, a potent inhibitor of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), has antibacterial and antimalaria activity. Due to its poor pharmacokinetics, more lipophilic DXR inhibitors are needed. However, the hydrophobic binding site( ...

    Fosmidomycin, a potent inhibitor of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), has antibacterial and antimalaria activity. Due to its poor pharmacokinetics, more lipophilic DXR inhibitors are needed. However, the hydrophobic binding site(s) in DXR remains elusive. Here, pyridine/quinoline containing phosphonates are identified to be DXR inhibitors with IC(50) values as low as 840 nM. We also report three DXR:inhibitor structures, revealing a novel binding mode. The indole group of Trp211 is found to move ~4.6 Å to open up a mainly hydrophobic pocket, where the pyridine/quinoline rings of the inhibitors are located and have strong π-π stacking/charge-transfer interactions with the indole. Docking studies demonstrate our structures could be used to predict the binding modes of other lipophilic DXR inhibitors. Overall, this work shows an important role of Trp211 in inhibitor recognition and provides a structural basis for future drug design and development.


    Organizational Affiliation

    Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B
420Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dxr (ispC, yaeM)
EC: 1.1.1.267
Find proteins for P45568 (Escherichia coli (strain K12))
Go to UniProtKB:  P45568
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SYC
Query on SYC

Download SDF File 
Download CCD File 
A, B
(pyridin-2-ylmethyl)phosphonic acid
C6 H8 N O3 P
WVWCWWLEFNGDBC-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SYCIC50: 4600 nM (100) BINDINGDB
SYCIC50: 4600 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 181.717α = 90.00
b = 59.298β = 90.00
c = 87.166γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
ADSCdata collection
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-10-19
    Type: Database references