Design and structural analysis of aromatic inhibitors of type II dehydroquinase from Mycobacterium tuberculosis - compound 41c [3-hydroxy-5-(3-nitrophenoxy)benzoic acid]

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 

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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. 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).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
153Mycobacterium tuberculosisMutation(s): 0 
Gene Names: aroDaroKaroQMT2612MTCY159.19Rv2537c
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1R2

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth D]
CA [auth E]
DA [auth F]
EA [auth G]
AA [auth C],
BA [auth D],
CA [auth E],
DA [auth F],
EA [auth G],
FA [auth H],
GA [auth I],
HA [auth J],
IA [auth K],
JA [auth L],
KA [auth N],
LA [auth O],
MA [auth P],
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]
3-hydroxy-5-(3-nitrophenoxy)benzoic acid
C13 H9 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.74α = 90
b = 139.69β = 96.43
c = 143.81γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

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