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- PDB-9i3y: CRYSTAL STRUCTURE OF HUMAN MONOACYLGLYCEROL LIPASE WITH COMPOUND 17 -

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Basic information

Entry
Database: PDB / ID: 9i3y
TitleCRYSTAL STRUCTURE OF HUMAN MONOACYLGLYCEROL LIPASE WITH COMPOUND 17
ComponentsMonoglyceride lipase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / SERINE ESTERASE
Function / homology
Function and homology information


Arachidonate production from DAG / Acyl chain remodeling of DAG and TAG / acylglycerol catabolic process / acylglycerol lipase / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / triglyceride catabolic process / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain ...Arachidonate production from DAG / Acyl chain remodeling of DAG and TAG / acylglycerol catabolic process / acylglycerol lipase / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / triglyceride catabolic process / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain / phosphatidylcholine lysophospholipase A1 activity / Triglyceride catabolism / regulation of signal transduction / lipid metabolic process / fatty acid biosynthetic process / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / regulation of inflammatory response / inflammatory response / endoplasmic reticulum membrane / protein homodimerization activity / membrane / plasma membrane / cytosol
Similarity search - Function
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Lipases, serine active site. / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Monoglyceride lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWalter, A. / Atz, K. / Stenzhorn, Y. / Nippa, D. / Grether, U. / Kuhn, B. / Martin, R. / Benz, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-dimensional optimization.
Authors: Nippa, D.F. / Atz, K. / Stenzhorn, Y. / Muller, A.T. / Tosstorff, A. / Benz, J. / Binch, H. / Burkler, M. / Haider, A. / Heer, D. / Hochstrasser, R. / Kramer, C. / Reutlinger, M. / ...Authors: Nippa, D.F. / Atz, K. / Stenzhorn, Y. / Muller, A.T. / Tosstorff, A. / Benz, J. / Binch, H. / Burkler, M. / Haider, A. / Heer, D. / Hochstrasser, R. / Kramer, C. / Reutlinger, M. / Schneider, P. / Shema, T. / Topp, A. / Walter, A. / Wittwer, M.B. / Wolfard, J. / Kuhn, B. / van der Stelt, M. / Martin, R.E. / Grether, U. / Schneider, G.
History
DepositionJan 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0424
Polymers35,4661
Non-polymers5773
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint7 kcal/mol
Surface area12140 Å2
Unit cell
Length a, b, c (Å)89.864, 126.920, 62.749
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

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Components

#1: Protein Monoglyceride lipase / MGL / HU-K5 / Lysophospholipase homolog / Lysophospholipase-like / Monoacylglycerol lipase / MAGL


Mass: 35465.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGLL / Production host: Escherichia coli (E. coli) / References: UniProt: Q99685, acylglycerol lipase
#2: Chemical ChemComp-A1IZ6 / 2-[4-[(2-pyridin-3-yl-1,3-benzoxazol-6-yl)carbonyl]piperazin-1-yl]-3~{H}-quinazolin-4-one


Mass: 452.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H20N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 11% PEG MME5K, 12% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.45→63.46 Å / Num. obs: 63798 / % possible obs: 99.9 % / Redundancy: 6.61 % / Biso Wilson estimate: 24.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.4
Reflection shellResolution: 1.45→1.55 Å / Rmerge(I) obs: 0.98 / Num. unique obs: 11432 / CC1/2: 0.676

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→44.62 Å / SU ML: 0.2575 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.4148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 3235 5.09 %
Rwork0.1758 60264 -
obs0.1776 63499 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.21 Å2
Refinement stepCycle: LAST / Resolution: 1.45→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 42 221 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472406
X-RAY DIFFRACTIONf_angle_d0.75573287
X-RAY DIFFRACTIONf_chiral_restr0.0715372
X-RAY DIFFRACTIONf_plane_restr0.0062418
X-RAY DIFFRACTIONf_dihedral_angle_d14.4209923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.50031450.53642550X-RAY DIFFRACTION97.89
1.47-1.490.52551350.50812570X-RAY DIFFRACTION98.61
1.49-1.520.49231470.48872543X-RAY DIFFRACTION98.82
1.52-1.550.47471170.44012605X-RAY DIFFRACTION99.09
1.55-1.570.43551400.39812593X-RAY DIFFRACTION99.6
1.57-1.60.33671410.36452600X-RAY DIFFRACTION99.31
1.6-1.640.36551500.33472589X-RAY DIFFRACTION99.46
1.64-1.670.36821240.2952586X-RAY DIFFRACTION99.71
1.67-1.710.30651490.28272602X-RAY DIFFRACTION99.67
1.71-1.750.26061310.25042632X-RAY DIFFRACTION99.46
1.75-1.80.26111500.23072585X-RAY DIFFRACTION99.49
1.8-1.850.25481270.22132614X-RAY DIFFRACTION99.6
1.85-1.910.2411640.18942582X-RAY DIFFRACTION99.71
1.91-1.980.24161270.16792624X-RAY DIFFRACTION99.85
1.98-2.060.1821500.15362600X-RAY DIFFRACTION99.89
2.06-2.160.19771560.15722636X-RAY DIFFRACTION99.61
2.16-2.270.18431440.15342621X-RAY DIFFRACTION99.75
2.27-2.410.18551250.15662648X-RAY DIFFRACTION99.71
2.41-2.60.21781390.1532639X-RAY DIFFRACTION99.96
2.6-2.860.19751360.15682671X-RAY DIFFRACTION99.93
2.86-3.270.19741560.15672657X-RAY DIFFRACTION100
3.27-4.120.19221380.13952700X-RAY DIFFRACTION99.96
4.12-44.620.16171440.14322817X-RAY DIFFRACTION99.87

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