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.

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9JX Query on 9JX Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
9JX	BindingDB: 5ZUN	IC50: 0.64 (nM) from 1 assay(s)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

Revision History (Full details and data files)

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