3RAS

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with a lipophilic phosphonate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase by lipophilic phosphonates: SAR, QSAR, and crystallographic studies.

Deng, L.Diao, J.Chen, P.Pujari, V.Yao, Y.Cheng, G.Crick, D.C.Prasad, B.V.Song, Y.

(2011) J.Med.Chem. 54: 4721-4734

  • DOI: 10.1021/jm200363d

  • PubMed Abstract: 
  • 1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) is a novel target for developing new antibacterial (including antituberculosis) and antimalaria drugs. Forty-one lipophilic phosphonates, representing a new class of DXR inhibitors, were synthesiz ...

    1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) is a novel target for developing new antibacterial (including antituberculosis) and antimalaria drugs. Forty-one lipophilic phosphonates, representing a new class of DXR inhibitors, were synthesized, among which 5-phenylpyridin-2-ylmethylphosphonic acid possesses the most activity against E. coli DXR (EcDXR) with a K(i) of 420 nM. Structure-activity relationships (SAR) are discussed, which can be rationalized using our EcDXR:inhibitor structures, and a predictive quantitative SAR (QSAR) model is also developed. Since inhibition studies of DXR from Mycobacterium tuberculosis (MtDXR) have not been performed well, 48 EcDXR inhibitors with a broad chemical diversity were found, however, to generally exhibit considerably reduced activity against MtDXR. The crystal structure of a MtDXR:inhibitor complex reveals the flexible loop containing the residues 198-208 has no strong interactions with the 3,4-dichlorophenyl group of the inhibitor, representing a structural basis for the reduced activity. Overall, these results provide implications in the future design and development of potent DXR inhibitors.


    Organizational Affiliation

    Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B
398Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: dxr
EC: 1.1.1.267
Find proteins for P9WNS1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNS1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
DCV
Query on DCV

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A, B
[(1R)-3-[acetyl(hydroxy)amino]-1-(3,4-dichlorophenyl)propyl]phosphonic acid
C11 H14 Cl2 N O5 P
ABGCTQYLJZGMBM-LLVKDONJSA-N
 Ligand Interaction
SO4
Query on SO4

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B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FM5
Query on FM5

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Download CCD File 
A, B
3-(N-HYDROXYACETAMIDO)-1-(3,4-DICHLOROPHENYL)PROPYLPHOSPHONIC ACID
C11 H14 Cl2 N O5 P
ABGCTQYLJZGMBM-NSHDSACASA-N
 Ligand Interaction
NDP
Query on NDP

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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 %)
DCVKi: 1500 nM (99) BINDINGDB
DCVKd: 360 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.250α = 90.00
b = 65.179β = 101.28
c = 85.408γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-07-25
    Type: Database references