5I7H

Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 6 [3-(3-(4-Bromophenyl)ureido)benzoic acid]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Inhibitors of the Cysteine Synthase CysM with Antibacterial Potency against Dormant Mycobacterium tuberculosis.

Brunner, K.Maric, S.Reshma, R.S.Almqvist, H.Seashore-Ludlow, B.Gustavsson, A.L.Poyraz, O.Yogeeswari, P.Lundback, T.Vallin, M.Sriram, D.Schnell, R.Schneider, G.

(2016) J Med Chem 59: 6848-6859

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00674
  • Primary Citation of Related Structures:  
    5I6D, 5I7A, 5I7H, 5I7O, 5I7R, 5IW8, 5IWC

  • PubMed Abstract: 

    Cysteine is an important amino acid in the redox defense of Mycobacterium tuberculosis, primarily as a building block of mycothiol. Genetic studies have implicated de novo cysteine biosynthesis in pathogen survival in infected macrophages, in particular for persistent M. tuberculosis. Here, we report on the identification and characterization of potent inhibitors of CysM, a critical enzyme in cysteine biosynthesis during dormancy. A screening campaign of 17 312 compounds identified ligands that bind to the active site with micromolar affinity. These were characterized in terms of their inhibitory potencies and structure-activity relationships through hit expansion guided by three-dimensional structures of enzyme-inhibitor complexes. The top compound binds to CysM with 300 nM affinity and displays selectivity over the mycobacterial homologues CysK1 and CysK2. Notably, two inhibitors show significant potency in a nutrient-starvation model of dormancy of Mycobacterium tuberculosis, with little or no cytotoxicity toward mammalian cells.


  • Organizational Affiliation

    Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet , S-171 77 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-phosphoserine sulfhydrylase
A, B, C, D
326Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: cysMRv1336MTCY130.21
EC: 2.5.1.113
UniProt
Find proteins for P9WP53 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WP53 
Go to UniProtKB:  P9WP53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WP53
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
68V
Query on 68V

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
3-{[(4-bromophenyl)carbamoyl]amino}benzoic acid
C14 H11 Br N2 O3
XLDDBXYVKMODRJ-UHFFFAOYSA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
M [auth D]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.591α = 94.33
b = 76.089β = 108.32
c = 80.716γ = 107.66
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description