5ZUN

Crystal structure of human monoacylglycerol lipase in complex with compound 3l

• PDB DOI: https://doi.org/10.2210/pdb5ZUN/pdb

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


• Deposited: 2018-05-08 Released: 2018-10-17 
• Deposition Author(s): Sogabe, S., Zama, Y., Lane, W., Snell, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.160 
• R-Value Work: 0.147 
• R-Value Observed: 0.148 

Starting Model: experimental

Literature

Design, Synthesis, and Evaluation of Piperazinyl Pyrrolidin-2-ones as a Novel Series of Reversible Monoacylglycerol Lipase Inhibitors

Aida, J., Fushimi, M., Kusumoto, T., Sugiyama, H., Arimura, N., Ikeda, S., Sasaki, M., Sogabe, S., Aoyama, K., Koike, T.

(2018) J Med Chem 61: 9205-9217

• PubMed: 30251836 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b00824
• Primary Citation of Related Structures:  
  5ZUN


• PubMed Abstract: 
  

  Monoacylglycerol lipase (MAGL) is a major serine hydrolase that hydrolyzes 2-arachidonoylglycerol (2-AG) to arachidonic acid (AA) and glycerol in the brain. Because 2-AG and AA are endogenous biologically active ligands in the brain, inhibition of MAGL is an attractive therapeutic target for CNS disorders, particularly neurodegenerative diseases. In this study, we report the structure-based drug design of novel piperazinyl pyrrolidin-2-ones starting from our hit compounds 2a and 2b. By enhancing the interaction of the piperazinyl pyrrolidin-2-one core and its substituents with the MAGL enzyme via design modifications, we identified a potent and reversible MAGL inhibitor, compound ( R)-3t. Oral administration of compound ( R)-3t to mice decreased AA levels and elevated 2-AG levels in the brain.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.53 kDa 
• Atom Count: 2,699 
• Modelled Residue Count: 289 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoglyceride lipase	A	305	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JX	B [auth A]	(4R)-1-(2'-chloro[1,1'-biphenyl]-3-yl)-4-[4-(1,3-thiazole-2-carbonyl)piperazin-1-yl]pyrrolidin-2-one C24 H23 Cl N4 O2 S OFKDHTKARMXLGB-LJQANCHMSA-N
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.160 
• R-Value Work: 0.147 
• R-Value Observed: 0.148 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.149	α = 90
b = 127.224	β = 90
c = 60.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Sogabe, S., Zama, Y., Lane, W., Snell, G.

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2018-11-07
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description