6GEO

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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Ligand Structure Quality Assessment 


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Literature

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: 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 ...

    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

    School of Pharmacy & Pharmaceutical Sciences Cardiff University King Edward VII Avenue Cardiff CF10 3NB U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mycocyclosin synthaseA396Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: cyp121MT2336
EC: 1.14.21.9 (PDB Primary Data), 1.14.19.70 (UniProt)
UniProt
Find proteins for P9WPP6 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P9WPP6 
Go to UniProtKB:  P9WPP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
EW2 (Subject of Investigation/LOI)
Query on EW2

Download Ideal Coordinates CCD File 
F [auth A]2-chloranyl-3-[4-(imidazol-1-ylmethyl)-1-phenyl-pyrazol-3-yl]-1~{H}-indole
C21 H16 Cl N5
RNSBGQRYBQOSEQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EW2 Binding MOAD:  6GEO Kd: 3310 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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