7ZIC | pdb_00007zic

Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.224 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid C26-monooxygenase
A, B, C
418Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cyp125cyp125A1Rv3545cMTCY03C7.11
EC: 1.14.15.29
UniProt
Find proteins for P9WPP1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP1 
Go to UniProtKB:  P9WPP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
T [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
5YG (Subject of Investigation/LOI)
Query on 5YG

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
S [auth C]
~{N}-[(4-methoxyphenyl)methyl]-4-(pyridin-4-ylmethyl)aniline
C20 H20 N2 O
FVAKBCRCJCQWCW-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
AA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth C],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.233α = 90
b = 68.684β = 93.968
c = 144.472γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2023-04-19
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2025-07-30
    Changes: Database references, Structure summary