Fumarate hydratase of Mycobacterium tuberculosis in complex with formate and allosteric modulator N-(5-(Azepan-1-ylsulfonyl)-2-methoxyphenyl)-2-(quinolin-4-yl)acetamide

Experimental Data Snapshot

  • Resolution: 1.44 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

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Targeting of Fumarate Hydratase fromMycobacterium tuberculosisUsing Allosteric Inhibitors with a Dimeric-Binding Mode.

Whitehouse, A.J.Libardo, M.D.J.Kasbekar, M.Brear, P.D.Fischer, G.Thomas, C.J.Barry 3rd, C.E.Boshoff, H.I.M.Coyne, A.G.Abell, C.

(2019) J Med Chem 62: 10586-10604

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01203
  • Primary Citation of Related Structures:  
    6S43, 6S7K, 6S7S, 6S7U, 6S7W, 6S7Z, 6S88

  • PubMed Abstract: 

    With the growing worldwide prevalence of antibiotic-resistant strains of tuberculosis (TB), new targets are urgently required for the development of treatments with novel modes of action. Fumarate hydratase (fumarase), a vulnerable component of the citric acid cycle in Mycobacterium tuberculosis ( Mtb ), is a metabolic target that could satisfy this unmet demand. A key challenge in the targeting of Mtb fumarase is its similarity to the human homolog, which shares an identical active site. A potential solution to this selectivity problem was previously found in a high-throughput screening hit that binds in a nonconserved allosteric site. In this work, a structure-activity relationship study was carried out with the determination of further structural biology on the lead series, affording derivatives with sub-micromolar inhibition. Further, the screening of this series against Mtb in vitro identified compounds with potent minimum inhibitory concentrations.

  • Organizational Affiliation

    Department of Biochemistry , University of Cambridge , Tennis Court Road , Cambridge , CB2 1GA , U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fumarate hydratase class II
A, B, C, D
474Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for P9WN93 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WN93 
Go to UniProtKB:  P9WN93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WN93
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
KZT Binding MOAD:  6S7W IC50: 4100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.44 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.682α = 90
b = 96.963β = 102.71
c = 124.736γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references