9G4M | pdb_00009g4m

Crystal structure of monoacylglycerol lipase with BODIPY labeled probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

A Highly Selective and Versatile Probe Platform for Visualization of Monoacylglycerol Lipase.

Hentsch, A.Guberman, M.Radetzki, S.Kaushik, S.Huizenga, M.Paul, J.Schippers, M.Benz, J.Kuhn, B.Heer, D.Topp, A.Esteves Gloria, L.Walter, A.Hochstrasser, R.Wittwer, M.B.von Kries, J.P.Collin, L.Blaising, J.van der Stelt, M.Lipstein, N.Grether, U.Nazare, M.

(2025) Angew Chem Int Ed Engl 64: e202413405-e202413405

  • DOI: https://doi.org/10.1002/anie.202413405
  • Primary Citation of Related Structures:  
    9G4M

  • PubMed Abstract: 

    Monoacylglycerol lipase (MAGL) is a key enzyme for signal termination in the endocannabinoid system (ECS). MAGL inhibition results in indirect activation of the cannabinoid receptors, which offers unique advantages for the treatment of, e.g., multiple sclerosis, epilepsy, and other neurological disorders. Molecular imaging techniques are valuable tools to overcome the current poor understanding of MAGL's distribution and role in patho- and physiological processes within ECS signaling. Herein, we report the design, synthesis, and validation of highly selective versatile fluorescent and click-chemistry probes for MAGL. Structure-based design combined with a reverse-design approach allowed the development of a structural unit that selectively and effectively recognizes MAGL while offering a versatile platform to attach different fluorophores and further reporter units. In this way, labeled probes with sub-nanomolar potency carrying diverse fluorescent dyes were obtained. Probe affinity and selectivity remained invariant to changes in the fluorophore subunit, showing the remarkable robustness of this platform in delivering tailor-made probes. Highly consistent inhibition across species supports pharmacological model translatability. Extensive profiling and validation in various cellular systems shows the ability of these highly potent and selective probes to elucidate the complex role of MAGL in ECS cellular signaling, inflammatory processes, and disease progression.


  • Organizational Affiliation
    • Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125, Berlin, GER.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Monoglyceride lipase323Homo sapiensMutation(s): 3 
Gene Names: MGLL
EC: 3.1.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q99685 (Homo sapiens)
Explore Q99685 
Go to UniProtKB:  Q99685
PHAROS:  Q99685
GTEx:  ENSG00000074416 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99685
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IIH (Subject of Investigation/LOI)
Query on A1IIH

Download Ideal Coordinates CCD File 
B [auth A]3-[2,2-bis(fluoranyl)-10,12-dimethyl-1$l^{4},3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaen-4-yl]-~{N}-[2-[2-[[2-[(6-oxidanylidene-7-oxa-2,5-diazaspiro[3.4]octan-2-yl)carbonyl]-2-azaspiro[3.3]heptan-6-yl]methyl]phenoxy]ethyl]propanamide
C35 H41 B F2 N6 O5
IREDGWRMCRGHGX-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.896α = 90
b = 127.245β = 90
c = 62.206γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release