7L4T

Crystal structure of human monoacylglycerol lipase in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
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
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 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
UUUUFICXTVCJQV-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
G [auth B],
H [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



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