Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP121A1 in complex with Triazole Pyrazole inhibitor 10j

  • Classification: OXIDOREDUCTASE
  • Organism(s): Mycobacterium tuberculosis CDC1551
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-04-27 Released: 2019-08-07 
  • Deposition Author(s): Levy, C.W.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council, Cancer Research UK, Medical Research Council (United Kingdom), Wellcome Trust

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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Design and Synthesis of Imidazole and Triazole Pyrazoles asMycobacterium TuberculosisCYP121A1 Inhibitors.

Kishk, S.M.McLean, K.J.Sood, S.Smith, D.Evans, J.W.D.Helal, M.A.Gomaa, M.S.Salama, I.Mostafa, S.M.de Carvalho, L.P.S.Levy, C.W.Munro, A.W.Simons, C.

(2019) ChemistryOpen 8: 995-1011

  • DOI: https://doi.org/10.1002/open.201900227
  • Primary Citation of Related Structures:  
    6GEO, 6GEQ

  • PubMed Abstract: 

    The emergence of untreatable drug-resistant strains of Mycobacterium tuberculosis is a major public health problem worldwide, and the identification of new efficient treatments is urgently needed. Mycobacterium tuberculosis cytochrome P450 CYP121A1 is a promising drug target for the treatment of tuberculosis owing to its essential role in mycobacterial growth. Using a rational approach, which includes molecular modelling studies, three series of azole pyrazole derivatives were designed through two synthetic pathways. The synthesized compounds were biologically evaluated for their inhibitory activity towards M. tuberculosis and their protein binding affinity ( K D ). Series 3 biarylpyrazole imidazole derivatives were the most effective with the isobutyl ( 10 f ) and tert -butyl ( 10 g ) compounds displaying optimal activity (MIC 1.562 μg/mL, K D 0.22 μM ( 10 f ) and 4.81 μM ( 10 g )). The spectroscopic data showed that all the synthesised compounds produced a type II red shift of the heme Soret band indicating either direct binding to heme iron or (where less extensive Soret shifts are observed) putative indirect binding via an interstitial water molecule. Evaluation of biological and physicochemical properties identified the following as requirements for activity: LogP >4, H-bond acceptors/H-bond donors 4/0, number of rotatable bonds 5-6, molecular volume >340 Å 3 , topological polar surface area <40 Å 2 .

  • Organizational Affiliation

    Manchester Institute of Biotechnology, School of Chemistry University of Manchester 131 Princess Street Manchester M1 7DN U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mycocyclosin synthase396Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: cyp121MT2336
EC: (PDB Primary Data), (UniProt)
Find proteins for P9WPP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP7 
Go to UniProtKB:  P9WPP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP7
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
EW2 Binding MOAD:  6GEO Kd: 3310 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.807α = 90
b = 77.807β = 90
c = 264.053γ = 120
Software Package:
Software NamePurpose
DIALSdata reduction
DIALSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-08-07 
  • Deposition Author(s): Levy, C.W.

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/I020160/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/I019227/1
Cancer Research UKUnited KingdomFC001060
Medical Research Council (United Kingdom)United KingdomFC001060
Wellcome TrustUnited KingdomFC001060
Wellcome TrustUnited Kingdom104785/B/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references