6T0J

Crystal structure of CYP124 in complex with SQ109


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450.

Bukhdruker, S.Varaksa, T.Grabovec, I.Marin, E.Shabunya, P.Kadukova, M.Grudinin, S.Kavaleuski, A.Gusach, A.Gilep, A.Borshchevskiy, V.Strushkevich, N.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21207683
  • Primary Citation of Related Structures:  
    6T0J

  • PubMed Abstract: 

    Spreading of the multidrug-resistant (MDR) strains of the one of the most harmful pathogen Mycobacterium tuberculosis (Mtb) generates the need for new effective drugs. SQ109 showed activity against resistant Mtb and already advanced to Phase II/III clinical trials. Fast SQ109 degradation is attributed to the human liver Cytochrome P450s (CYPs). However, no information is available about interactions of the drug with Mtb CYPs. Here, we show that Mtb CYP124, previously assigned as a methyl-branched lipid monooxygenase, binds and hydroxylates SQ109 in vitro. A 1.25 Å-resolution crystal structure of the CYP124-SQ109 complex unambiguously shows two conformations of the drug, both positioned for hydroxylation of the ω-methyl group in the trans position. The hydroxylated SQ109 presumably forms stabilizing H-bonds with its target, Mycobacterial membrane protein Large 3 (MmpL3). We anticipate that Mtb CYPs could function as analogs of drug-metabolizing human CYPs affecting pharmacokinetics and pharmacodynamics of antitubercular (anti-TB) drugs.


  • Organizational Affiliation

    Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-branched lipid omega-hydroxylase435Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cyp124Rv2266MTCY339.44c
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 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
RWZ (Subject of Investigation/LOI)
Query on RWZ

Download Ideal Coordinates CCD File 
C [auth A]N-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine
C22 H38 N2
JFIBVDBTCDTBRH-MDXVBTBDSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
F [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
L [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.54α = 90
b = 75.11β = 106.84
c = 56.59γ = 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
Russian Foundation for Basic ResearchRussian Federation20-54-00005
Belarusian Republican Foundation for Fundamental ResearchBelarusB20R-061
Ministry of Science and Higher Education of the Russian FederationRussian Federation075-00337-20-03 (FSMG-2020-0003)

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2020-11-04
    Changes: Author supporting evidence, Database references
  • Version 2.0: 2021-02-17
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description