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- PDB-7l50: Crystal structure of human monoacylglycerol lipase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7l50
TitleCrystal structure of human monoacylglycerol lipase in complex with compound 4f
ComponentsMonoglyceride lipase
KeywordsHYDROLASE/INHIBITOR / Inhibitor / Serine hydrolase / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


regulation of retrograde trans-synaptic signaling by endocanabinoid / acylglycerol lipase / varicosity / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / cerebellar climbing fiber to Purkinje cell synapse / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain / long-term synaptic depression ...regulation of retrograde trans-synaptic signaling by endocanabinoid / acylglycerol lipase / varicosity / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / cerebellar climbing fiber to Purkinje cell synapse / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain / long-term synaptic depression / regulation of axon extension / parallel fiber to Purkinje cell synapse / presynapse / regulation of inflammatory response / membrane / cytosol
Similarity search - Function
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ACETATE ION / Chem-XOM / Monoglyceride lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsQin, L. / Lane, W. / Skene, R.J.
CitationJournal: J.Med.Chem. / Year: 2021
Title: 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.
Authors: 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. / ...Authors: 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.
History
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Sep 15, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoglyceride lipase
B: Monoglyceride lipase
C: Monoglyceride lipase
D: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,86916
Polymers140,9374
Non-polymers1,93212
Water2,828157
1
A: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7174
Polymers35,2341
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7174
Polymers35,2341
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7174
Polymers35,2341
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7174
Polymers35,2341
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.894, 127.168, 119.675
Angle α, β, γ (deg.)90.000, 73.673, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Monoglyceride lipase


Mass: 35234.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGLL / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C4DFN3
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-XOM / (2s,4R)-2-{3-[(3-chloro-4-methylphenyl)methoxy]azetidine-1-carbonyl}-7-oxa-5-azaspiro[3.4]octan-6-one


Mass: 364.823 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H21ClN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaOAc pH 5.5, 32-38% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.06 Å / Num. obs: 79270 / % possible obs: 98.9 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.072 / Rrim(I) all: 0.143 / Net I/σ(I): 4.1
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.728 / Num. unique obs: 4493 / CC1/2: 0.868 / Rpim(I) all: 0.439 / Rrim(I) all: 0.854 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZUN

5zun


Resolution: 2.3→48.191 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 31.945 / SU ML: 0.304 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.222
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2689 3834 4.895 %
Rwork0.2392 74488 -
all0.241 --
obs-78322 97.734 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 82.049 Å2
Baniso -1Baniso -2Baniso -3
1--2.257 Å2-0 Å2-2.694 Å2
2---8.109 Å2-0 Å2
3---7.501 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8864 0 132 157 9153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129209
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.64512504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9651138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52821.743436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.327151506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9031555
X-RAY DIFFRACTIONr_chiral_restr0.0880.21150
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027046
X-RAY DIFFRACTIONr_nbd_refined0.2140.24378
X-RAY DIFFRACTIONr_nbtor_refined0.3030.26274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2307
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.210
X-RAY DIFFRACTIONr_mcbond_it2.5644.3224584
X-RAY DIFFRACTIONr_mcangle_it4.2756.4565706
X-RAY DIFFRACTIONr_scbond_it2.9184.3464625
X-RAY DIFFRACTIONr_scangle_it4.7086.4636782
X-RAY DIFFRACTIONr_lrange_it8.9957.70713707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.4062910.4425379X-RAY DIFFRACTION95.858
2.36-2.4240.4332680.4075255X-RAY DIFFRACTION95.9687
2.424-2.4940.4292860.4065101X-RAY DIFFRACTION96.0935
2.494-2.5710.4182500.3574952X-RAY DIFFRACTION96.7454
2.571-2.6550.3442380.3174859X-RAY DIFFRACTION96.6622
2.655-2.7480.3272550.34684X-RAY DIFFRACTION96.8621
2.748-2.8520.2722220.2774565X-RAY DIFFRACTION96.7657
2.852-2.9680.3222070.2514392X-RAY DIFFRACTION97.6848
2.968-3.0990.3012200.2594237X-RAY DIFFRACTION98.3017
3.099-3.250.2412150.2244069X-RAY DIFFRACTION98.3697
3.25-3.4250.2812040.2363886X-RAY DIFFRACTION98.7446
3.425-3.6320.2482020.2193682X-RAY DIFFRACTION99.0311
3.632-3.8810.2161530.2043501X-RAY DIFFRACTION99.5098
3.881-4.1910.2021750.1983271X-RAY DIFFRACTION99.6818
4.191-4.5880.2051320.1733015X-RAY DIFFRACTION99.4313
4.588-5.1250.1991400.1662690X-RAY DIFFRACTION99.4378
5.125-5.9090.2691290.22395X-RAY DIFFRACTION99.5268
5.909-7.2170.2461010.2122050X-RAY DIFFRACTION99.5833
7.217-10.1190.2341030.1751579X-RAY DIFFRACTION99.8812
10.119-48.1910.164430.187927X-RAY DIFFRACTION99.0807
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54470.06060.1752.35010.38060.1320.0227-0.03380.2427-0.12-0.06880.03030.0438-0.00310.04610.19330.00670.06490.44650.01690.649697.6509-33.2935167.5382
20.56930.1347-0.08612.75960.31140.06040.08970.0574-0.18420.1766-0.0694-0.1183-0.0268-0.0127-0.02040.1814-0.00320.06220.42450.00340.6677129.0034-11.2513177.2518
30.7863-0.25950.22122.1775-0.27970.09940.1012-0.02020.23420.049-0.12070.00630.04780.01150.01950.7744-0.01920.48440.0385-0.03130.4616112.223527.7195119.7576
40.86440.1649-0.07532.70540.06110.0120.087-0.0265-0.1880.0934-0.0984-0.0162-0.03750.00020.01140.8088-0.00790.51470.01750.00670.4391112.3432-13.7347119.5722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 701
2X-RAY DIFFRACTION2ALLB1 - 701
3X-RAY DIFFRACTION3ALLC1 - 701
4X-RAY DIFFRACTION4ALLD1 - 701

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