Crystal structure of M. tuberculosis EchA6 bound to ligand GSK366A

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria.

Cox, J.A.Abrahams, K.A.Alemparte, C.Ghidelli-Disse, S.Rullas, J.Angulo-Barturen, I.Singh, A.Gurcha, S.S.Nataraj, V.Bethell, S.Remuinan, M.J.Encinas, L.Jervis, P.J.Cammack, N.C.Bhatt, A.Kruse, U.Bantscheff, M.Futterer, K.Barros, D.Ballell, L.Drewes, G.Besra, G.S.

(2016) Nat Microbiol 1: 15006-15006

  • DOI: https://doi.org/10.1038/nmicrobiol.2015.6
  • Primary Citation of Related Structures:  
    5DTP, 5DTW, 5DU4, 5DU6, 5DU8, 5DUC, 5DUF

  • PubMed Abstract: 

    Phenotypic screens for bactericidal compounds against drug-resistant tuberculosis are beginning to yield novel inhibitors. However, reliable target identification remains challenging. Here, we show that tetrahydropyrazo[1,5-a]pyrimidine-3-carboxamide (THPP) selectively pulls down EchA6 in a stereospecific manner, instead of the previously assigned target Mycobacterium tuberculosis MmpL3. While homologous to mammalian enoyl-coenzyme A (CoA) hydratases, EchA6 is non-catalytic yet essential and binds long-chain acyl-CoAs. THPP inhibitors compete with CoA-binding, suppress mycolic acid synthesis, and are bactericidal in a mouse model of chronic tuberculosis infection. A point mutation, W133A, abrogated THPP-binding and increased both the in vitro minimum inhibitory concentration and the in vivo effective dose 99 in mice. Surprisingly, EchA6 interacts with selected enzymes of fatty acid synthase II (FAS-II) in bacterial two-hybrid assays, suggesting essentiality may be linked to feeding long-chain fatty acids to FAS-II. Finally, our data show that spontaneous resistance-conferring mutations can potentially obscure the actual target or alternative targets of small molecule inhibitors.

  • Organizational Affiliation

    Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable enoyl-CoA hydratase echA6263Mycobacterium tuberculosisMutation(s): 0 
Gene Names: echA6Rv0905MTCY31.33
Find proteins for P9WNP1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNP1 
Go to UniProtKB:  P9WNP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNP1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5FF

Download Ideal Coordinates CCD File 
B [auth A](5R,7S)-5-(4-ethylphenyl)-N-(4-methoxybenzyl)-7-(trifluoromethyl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide
C24 H25 F3 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
5FF Binding MOAD:  5DU4 Kd: 5600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.83α = 90
b = 94.83β = 90
c = 87.51γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description