5OEL

Mycobacterium tuberculosis DprE1 mutant Y314C in complex with TCA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Determinants of the Inhibition of DprE1 and CYP2C9 by Antitubercular Thiophenes.

Liu, R.Lyu, X.Batt, S.M.Hsu, M.H.Harbut, M.B.Vilcheze, C.Cheng, B.Ajayi, K.Yang, B.Yang, Y.Guo, H.Lin, C.Gan, F.Wang, C.Franzblau, S.G.Jacobs, W.R.Besra, G.S.Johnson, E.F.Petrassi, M.Chatterjee, A.K.Futterer, K.Wang, F.

(2017) Angew Chem Int Ed Engl 56: 13011-13015

  • DOI: https://doi.org/10.1002/anie.201707324
  • Primary Citation of Related Structures:  
    5OEL, 5OEP, 5OEQ, 5W0C

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) DprE1, an essential isomerase for the biosynthesis of the mycobacterial cell wall, is a validated target for tuberculosis (TB) drug development. Here we report the X-ray crystal structures of DprE1 and the DprE1 resistant mutant (Y314C) in complexes with TCA1 derivatives to elucidate the molecular basis of their inhibitory activities and an unconventional resistance mechanism, which enabled us to optimize the potency of the analogs. The selected lead compound showed excellent in vitro and in vivo activities, and low risk of toxicity profile except for the inhibition of CYP2C9. A crystal structure of CYP2C9 in complex with a TCA1 analog revealed the similar interaction patterns to the DprE1-TCA1 complex. Guided by the structures, an optimized molecule was generated with differential inhibitory activities against DprE1 and CYP2C9, which provides insights for development of a clinical candidate to treat TB.


  • Organizational Affiliation

    California Institute for Biomedical Research (Calibr), La Jolla, CA, 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Decaprenylphosphoryl-beta-D-ribose oxidase
A, B
477Mycobacterium tuberculosis CDC1551Mutation(s): 1 
Gene Names: dprE1MT3898
EC: 1.1.98.3
UniProt
Find proteins for P9WJF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJF1 
Go to UniProtKB:  P9WJF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJF1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.61α = 90
b = 83.77β = 103.18
c = 80.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/K012118/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description