9F8C | pdb_00009f8c

Crystal structure of human monoacylglycerol lipase in complex with compound 7m

• PDB DOI: https://doi.org/10.2210/pdb9F8C/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-05-06 Released: 2025-01-22 
• Deposition Author(s): Kuhn, B., Ritter, M., Hornsperger, B., Bell, C., Kocer, B., Rombach, D., Richter, H., Grether, U., Gobbi, L., Kuratli, M., Collin, L., Benz, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Discovery of cis -Hexahydro-pyrido-oxazinones as Reversible, Drug-like Monoacylglycerol Lipase Inhibitors.

Kuhn, B., Ritter, M., Hornsperger, B., Bell, C., Kocer, B., Rombach, D., Lutz, M.D.R., Gobbi, L., Kuratli, M., Bartelmus, C., Burkler, M., Koller, R., Tosatti, P., Ruf, I., Guerard, M., Pavlovic, A., Stephanus, J., O'Hara, F., Wetzl, D., Saal, W., Stihle, M., Roth, D., Hug, M., Huber, S., Heer, D., Kroll, C., Topp, A., Schneider, M., Gertsch, J., Glasmacher, S., van der Stelt, M., Martella, A., Wittwer, M.B., Collin, L., Benz, J., Richter, H., Grether, U.

(2024) J Med Chem 67: 18448-18464

• PubMed: 39360636 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c01769
• Primary Citation of Related Structures:  
  9F8A, 9F8B, 9F8C, 9F8D


• PubMed Abstract: 
  

  Monoacylglycerol lipase (MAGL) is a key enzyme involved in the metabolism of the endogenous signaling ligand 2-arachidonoylglycerol, a neuroprotective endocannabinoid intimately linked to central nervous system (CNS) disorders associated with neuroinflammation. In the quest for novel MAGL inhibitors, a focused screening approach on a Roche library subset provided a reversible benzoxazinone hit exhibiting high ligand efficiency. The subsequent design of the three-dimensional cis -hexahydro-pyrido-oxazinone ( cis -HHPO) moiety as benzoxazinone replacement enabled the combination of high MAGL potency with favorable ADME properties. Through enzymatic resolution an efficient synthetic route of the privileged cis -(4 R ,8 S ) HHPO headgroup was established, providing access to the highly potent and selective MAGL inhibitor 7o . Candidate molecule 7o matches the target compound profile of CNS drugs as it achieves high CSF exposures after systemic administration in rodents. It engages with the target in the brain and modulates neuroinflammatory processes, thus holding great promise for the treatment of CNS disorders.

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Organizational Affiliation: 
• Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland.
Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bern 3012, Switzerland.
Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Leiden 2300 CC, Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.06 kDa 
• Atom Count: 2,741 
• Modeled Residue Count: 295 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoglyceride lipase	A	323	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IA2 (Subject of Investigation/LOI)	B [auth A]	(4~{a}~{R},8~{a}~{R})-6-[4-[[4-(trifluoromethyl)phenyl]methyl]piperidin-1-yl]carbonyl-4,4~{a},5,7,8,8~{a}-hexahydropyrido[4,3-b][1,4]oxazin-3-one C21 H26 F3 N3 O3 YUPLWIRVNVZRHU-QZTJIDSGSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.991	α = 90
b = 127.429	β = 90
c = 62.593	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SADABS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Kuhn, B., Ritter, M., Hornsperger, B., Bell, C., Kocer, B., Rombach, D., Richter, H., Grether, U., Gobbi, L., Kuratli, M., Collin, L., Benz, J.

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Funding Organization	Location	Grant Number
Not funded	Switzerland	--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release