7L4W | pdb_00007l4w

Crystal structure of human monoacylglycerol lipase in complex with compound 2d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.221 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.186 (Depositor) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 71.26 kDa 
  • Atom Count: 4,642 
  • Modeled Residue Count: 578 
  • Deposited Residue Count: 640 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Monoglyceride lipase
A, B
320Homo sapiensMutation(s): 0 
Gene Names: MGLL
EC: 3.1.1.23
Membrane Entity: Yes 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XOV
(Subject of Investigation/LOI)

Query on XOV



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(2s,4R)-2-{4-[(2-chloro-4-fluorophenoxy)methyl]piperidine-1-carbonyl}-7-oxa-5-azaspiro[3.4]octan-6-one
C19 H22 Cl F N2 O4
ZXSYTHGPTJFVMM-XVDXERDNSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
XOV BindingDB:  7L4W IC50: 3.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.221 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.186 (Depositor) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.623α = 90
b = 127.215β = 90
c = 135.961γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

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