Crystal structure of human monoacylglycerol lipase in complex with compound 1

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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This is version 1.3 of the entry. See complete history


Design and Synthesis of Novel Spiro Derivatives as Potent and Reversible Monoacylglycerol Lipase (MAGL) Inhibitors: Bioisosteric Transformation from 3-Oxo-3,4-dihydro-2 H -benzo[ b ][1,4]oxazin-6-yl Moiety.

Ikeda, S.Sugiyama, H.Tokuhara, H.Murakami, M.Nakamura, M.Oguro, Y.Aida, J.Morishita, N.Sogabe, S.Dougan, D.R.Gay, S.C.Qin, L.Arimura, N.Takahashi, Y.Sasaki, M.Kamada, Y.Aoyama, K.Kimoto, K.Kamata, M.

(2021) J Med Chem 64: 11014-11044

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00432
  • Primary Citation of Related Structures:  
    7L4T, 7L4U, 7L4W, 7L50

  • PubMed Abstract: 

    The therapeutic potential of monoacylglycerol lipase (MAGL) inhibitors in central nervous system-related diseases has attracted attention worldwide. However, the availability of reversible-type inhibitor is still limited to clarify the pharmacological effect. Herein, we report the discovery of novel spiro chemical series as potent and reversible MAGL inhibitors with a different binding mode to MAGL using Arg57 and His121. Starting from hit compound 1 and its co-crystal structure with MAGL, structure-based drug discovery (SBDD) approach enabled us to generate various spiro scaffolds like 2a (azetidine-lactam), 2b (cyclobutane-lactam), and 2d (cyclobutane-carbamate) as novel bioisosteres of 3-oxo-3,4-dihydro-2 H -benzo[ b ][1,4]oxazin-6-yl moiety in 1 with higher lipophilic ligand efficiency (LLE). Optimization of the left hand side afforded 4f as a promising reversible MAGL inhibitor, which showed potent in vitro MAGL inhibitory activity (IC 50 6.2 nM), good oral absorption, blood-brain barrier penetration, and significant pharmacodynamic changes (2-arachidonoylglycerol increase and arachidonic acid decrease) at 0.3-10 mg/kg, po. in mice.

  • Organizational Affiliation

    Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Monoglyceride lipase
A, B
320Homo sapiensMutation(s): 0 
Gene Names: MGLL
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XPD (Subject of Investigation/LOI)
Query on XPD

Download Ideal Coordinates CCD File 
C [auth A]6-{4-[(2-chloro-4-fluorophenoxy)methyl]piperidine-1-carbonyl}-2H-1,4-benzoxazin-3(4H)-one
C21 H20 Cl F N2 O4
Query on MPD

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
G [auth B],
H [auth B]
C6 H14 O2
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.818α = 90
b = 127.378β = 90
c = 136.084γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2021-10-20
    Changes: Structure summary
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description