7QQ7 | pdb_00007qq7

Crystal structure of CYP142 from Mycobacterium tuberculosis in complex with an inhibitor at partial occupancy with PEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Fragment-Based Development of Small Molecule Inhibitors Targeting Mycobacterium tuberculosis Cholesterol Metabolism.

Kavanagh, M.E.McLean, K.J.Gilbert, S.H.Amadi, C.N.Snee, M.Tunnicliffe, R.B.Arora, K.Boshoff, H.I.M.Fanourakis, A.Rebollo-Lopez, M.J.Ortega, F.Levy, C.W.Munro, A.W.Leys, D.Abell, C.Coyne, A.G.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00478
  • Primary Citation Related Structures: 
    7P5T, 7QQ7, 7ZGL, 7ZIC, 8S4M, 8S53

  • PubMed Abstract: 

    Tuberculosis is the deadliest infectious disease in history and new drugs are urgently required to combat multidrug-resistant (MDR) strains of Mycobacterium tuberculosis ( Mtb ). Here, we exploit the relience of Mtb on host-derived cholesterol to develop a novel class of antitubercular compounds that target Mtb CYP125 and CYP142; the enzymes that catalyze the first step of cholesterol metabolism. A combination of fragment screening and structure-based drug design was used to identify a hit compound and guide synthetic optimization of a dual CYP125/142 ligand 5m ( K D 40-160 nM), which potently inhibits enzyme activity in vitro ( K I < 100 nM), and the growth of Mtb in extracellular (MIC 99 0.4-1.5 μM) and intracellular assays (IC 50 1.7 μM). The structural data and lead compounds reported here will help study Mtb cholesterol metabolism and guide the development of novel antibiotics to combat MDR Mtb.


  • Organizational Affiliation
    • Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.

Macromolecule Content 

  • Total Structure Weight: 45.88 kDa 
  • Atom Count: 3,824 
  • Modeled Residue Count: 396 
  • Deposited Residue Count: 398 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Steroid C26-monooxygenase398Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cyp142cyp142A1Rv3518cMTV023.25c
EC: 1.14.15.28
UniProt
Find proteins for P9WPL5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPL5 
Go to UniProtKB:  P9WPL5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPL5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / 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
EIQ
(Subject of Investigation/LOI)

Query on EIQ



Download:Ideal Coordinates CCD File
J [auth A]~{N}-[4-(pyridin-4-ylmethyl)phenyl]benzenesulfonamide
C18 H16 N2 O2 S
CFLHYDJOEWYNKS-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
D [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.308α = 90
b = 65.191β = 90
c = 128.409γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2025-07-30
    Changes: Database references, Structure summary