5W0C

Cytochrome P450 (CYP) 2C9 TCA007 Inhibitor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


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: 10.1002/anie.201707324
  • Primary Citation of Related Structures:  

  • 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 resis ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2C9
A
477Homo sapiensMutation(s): 0 
Gene Names: CYP2C9 (CYP2C10)
EC: 1.14.14.-
Find proteins for P11712 (Homo sapiens)
Go to Gene View: CYP2C9
Go to UniProtKB:  P11712
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9W6
Query on 9W6

Download SDF File 
Download CCD File 
A
ethyl {2-[([1,3]thiazolo[4,5-c]pyridine-2-carbonyl)amino]thiophene-3-carbonyl}carbamate
C15 H12 N4 O4 S2
JCOQDKZVKXILLW-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 91.394α = 90.00
b = 91.394β = 90.00
c = 169.225γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM031001

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references