7ZB9

Crystal structure of CYP124 in complex with inhibitor carbethoxyhexyl imidazole in the absence of glycerol (NoCryo)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural insights into the effects of glycerol on ligand binding to cytochrome P450.

Bukhdruker, S.Varaksa, T.Orekhov, P.Grabovec, I.Marin, E.Kapranov, I.Kovalev, K.Astashkin, R.Kaluzhskiy, L.Ivanov, A.Mishin, A.Rogachev, A.Gordeliy, V.Gilep, A.Strushkevich, N.Borshchevskiy, V.

(2023) Acta Crystallogr D Struct Biol 79: 66-77

  • DOI: https://doi.org/10.1107/S2059798322011019
  • Primary Citation of Related Structures:  
    7ZB9

  • PubMed Abstract: 

    New antitubercular drugs are vital due to the spread of resistant strains. Carbethoxyhexyl imidazole (CHImi) inhibits cytochrome P450 CYP124, which is a steroid-metabolizing enzyme that is important for the survival of Mycobacterium tuberculosis in macrophages. The available crystal structure of the CYP124-CHImi complex reveals two glycerol molecules in the active site. A 1.15 Å resolution crystal structure of the glycerol-free CYP124-CHimi complex reported here shows multiple conformations of CHImi and the CYP124 active site which were previously restricted by glycerol. Complementary molecular dynamics simulations show coherence of the ligand and enzyme conformations. Spectrophotometric titration confirmed the influence of glycerol on CHImi binding: the affinity decreases more than tenfold in glycerol-containing buffer. In addition, it also showed that glycerol has a similar effect on other azole and triazole CYP124 ligands. Together, these data show that glycerol may compromise structural-functional studies and impede rational drug-design campaigns.


  • Organizational Affiliation

    Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYP124 in complex with inhibitor carbethoxyhexyl imidazole435Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 1.14.15.14 (PDB Primary Data), 1.14.15.28 (PDB Primary Data)
UniProt
Find proteins for P9WPP3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP3 
Go to UniProtKB:  P9WPP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP3
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 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
M65 (Subject of Investigation/LOI)
Query on M65

Download Ideal Coordinates CCD File 
C [auth A]ethyl 7-imidazol-1-ylheptanoate
C12 H20 N2 O2
IGQBGUMGRVQYDB-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL
Query on CL

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

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.54α = 90
b = 75.08β = 106.957
c = 56.56γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education and Science of the Russian FederationRussian Federation075-15-2021-1354

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-03-27
    Changes: Database references