4KIW

Design and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from Mycobacterium tuberculosis - compound 49e [5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid]

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.202 

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Literature

Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase from Mycobacterium tuberculosis.

Howard, N.I., Dias, M.V., Peyrot, F., Chen, L., Schmidt, M.F., Blundell, T.L., Abell, C.

(2015) ChemMedChem 10: 116-133

  • DOI: https://doi.org/10.1002/cmdc.201402298
  • Primary Citation of Related Structures:  
    4KI7, 4KIJ, 4KIU, 4KIW

  • PubMed Abstract: 

    • 3-Dehydroquinase, the third enzyme in the shikimate pathway, is a potential target for drugs against tuberculosis. Whilst a number of potent inhibitors of the Mycobacterium tuberculosis enzyme based on a 3-dehydroquinate core have been identified, they generally show little or no in vivo activity, and were synthetically complex to prepare ...

    3-Dehydroquinase, the third enzyme in the shikimate pathway, is a potential target for drugs against tuberculosis. Whilst a number of potent inhibitors of the Mycobacterium tuberculosis enzyme based on a 3-dehydroquinate core have been identified, they generally show little or no in vivo activity, and were synthetically complex to prepare. This report describes studies to develop tractable and drug-like aromatic analogues of the most potent inhibitors. A range of carbon-carbon linked biaryl analogues were prepared to investigate the effect of hydrogen bond acceptor and donor patterns on inhibition. These exhibited inhibitory activity in the high-micromolar range. The addition of flexible linkers in the compounds led to the identification of more potent 3-nitrobenzylgallate- and 5-aminoisophthalate-based analogues.

    Organizational Affiliation: 

    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK).



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-dehydroquinate dehydratase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
167Mycobacterium tuberculosisMutation(s): 0 
Gene Names: aroD, aroQ, MT2612, MTCY159.19, Rv2537c
EC: 4.2.1.10
UniProt
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPX7 
Go to UniProtKB:  P9WPX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPX7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KIW
Query on KIW
Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth D]
CA [auth E]
DA [auth G]
EA [auth H]
AA [auth C],
BA [auth D],
CA [auth E],
DA [auth G],
EA [auth H],
FA [auth J],
GA [auth K],
HA [auth L],
IA [auth M],
JA [auth N],
KA [auth O],
LA [auth P],
MA [auth Q],
NA [auth R],
OA [auth S],
PA [auth T],
QA [auth U],
RA [auth V],
SA [auth W],
TA [auth X],
Y [auth A],
Z [auth B]
5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid
C15 H12 N2 O6
OJGIZUUIUXRITB-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.71α = 90
b = 135.22β = 97.18
c = 143.91γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2015-01-07
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary