6S7U

Fumarate hydratase of Mycobacterium tuberculosis in complex with formate and allosteric modulator N-(5-(Azepan-1-ylsulfonyl)-2-methoxyphenyl)-2-(1H-indol-3-yl)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 ...

    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 Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate hydratase class IIA, B, C, D474Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 4.2.1.2
UniProt
Find proteins for P9WN93 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WN93 
Go to UniProtKB:  P9WN93
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KZK
Query on KZK

Download Ideal Coordinates CCD File 
E [auth A], H [auth C]~{N}-[5-(azepan-1-ylsulfonyl)-2-methoxy-phenyl]-2-(1~{H}-indol-3-yl)ethanamide
C23 H27 N3 O4 S
WUSKETSOXMZDPT-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
F [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth B], I [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.258α = 90
b = 96.662β = 102.75
c = 124.259γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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