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- PDB-9rhw: M. tuberculosis meets European Lead Factory: identification and s... -

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Basic information

Entry
Database: PDB / ID: 9rhw
TitleM. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography: ELF1
ComponentsMonoacylglycerol lipase
KeywordsHYDROLASE / Rv0183 / Inhibitor / Monoacylglycerol lipase
Function / homology
Function and homology information


glycerolipid catabolic process / acylglycerol lipase / lipase activity / monoacylglycerol lipase activity / peptidoglycan-based cell wall / symbiont-mediated activation of host apoptosis / extracellular region / membrane / plasma membrane
Similarity search - Function
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / ETHANOL / PHOSPHATE ION / Monoacylglycerol lipase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsRiegler-Berket, L. / Goedl, L. / Oberer, M. / Sagmeister, T.
Funding support Austria, 3items
OrganizationGrant numberCountry
Austrian Science FundF73 Austria
Austrian Science FundDOC 50 Austria
Austrian Science FundDOC 130 Austria
CitationJournal: Disease and Therapeutics / Year: 2025
Title: M. tuberculosis meets European lead factory:Identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography
Authors: Riegler-Berket, L. / Godl, L. / Polidori, N. / Aschauer, P. / Grininger, C. / Prosser, G. / Lichtenegger, J. / Sagmeister, T. / Parigger, L. / Gruber, C.C. / Reiling, N. / Oberer, M.
History
DepositionJun 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,68410
Polymers33,6761
Non-polymers1,0089
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Monoacylglycerol lipase
hetero molecules

A: Monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,36720
Polymers67,3522
Non-polymers2,01518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area3780 Å2
ΔGint-46 kcal/mol
Surface area20790 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-4 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.485, 82.535, 90.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Monoacylglycerol lipase / MGL


Mass: 33676.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv0183 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O07427, acylglycerol lipase

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Non-polymers , 7 types, 286 molecules

#2: Chemical ChemComp-7WW / [5-(2-chlorophenyl)-1-(4-methoxyphenyl)pyrazol-3-yl]-[(3R)-3-oxidanylpyrrolidin-1-yl]methanone


Mass: 397.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 1000, PEG 3350, MPD, HEPES, MOPS, CHAPS, CHAPSO, Sodium glycocholate hydrate, Taurocholic acid sodium salt hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03272 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03272 Å / Relative weight: 1
ReflectionResolution: 1.25→45.3 Å / Num. obs: 83281 / % possible obs: 98.22 % / Redundancy: 2 % / Biso Wilson estimate: 13.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.92
Reflection shellResolution: 1.25→1.295 Å / Num. unique obs: 7252 / CC1/2: 0.857

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Processing

Software
NameVersionClassification
REFMACRefmac5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→45.3 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / Phase error: 14.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1549 4142 4.97 %
Rwork0.139 --
obs0.1398 83267 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 66 277 2473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122600
X-RAY DIFFRACTIONf_angle_d1.413597
X-RAY DIFFRACTIONf_dihedral_angle_d12.262458
X-RAY DIFFRACTIONf_chiral_restr0.096396
X-RAY DIFFRACTIONf_plane_restr0.027489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.2551280.21712179X-RAY DIFFRACTION82
1.26-1.280.18631220.20022333X-RAY DIFFRACTION88
1.28-1.290.21861080.18642382X-RAY DIFFRACTION90
1.29-1.310.21951370.18572465X-RAY DIFFRACTION93
1.31-1.330.19781410.17092579X-RAY DIFFRACTION98
1.33-1.350.17881350.16682658X-RAY DIFFRACTION99
1.35-1.370.17641280.15692621X-RAY DIFFRACTION100
1.37-1.390.19251470.15212648X-RAY DIFFRACTION100
1.39-1.410.14581340.15012649X-RAY DIFFRACTION100
1.41-1.430.15391420.14922643X-RAY DIFFRACTION100
1.43-1.460.15741410.14942675X-RAY DIFFRACTION100
1.46-1.480.16011460.15452660X-RAY DIFFRACTION100
1.48-1.510.18281290.14832646X-RAY DIFFRACTION100
1.51-1.540.15961410.1352648X-RAY DIFFRACTION100
1.54-1.570.14811360.13282673X-RAY DIFFRACTION100
1.57-1.610.15531500.12492680X-RAY DIFFRACTION100
1.61-1.650.15271530.12182644X-RAY DIFFRACTION100
1.65-1.70.14011400.12812653X-RAY DIFFRACTION100
1.7-1.750.14111350.13132684X-RAY DIFFRACTION100
1.75-1.80.15041250.12992687X-RAY DIFFRACTION100
1.8-1.870.13211390.13552674X-RAY DIFFRACTION100
1.87-1.940.14671400.12912680X-RAY DIFFRACTION100
1.94-2.030.14051570.12032682X-RAY DIFFRACTION100
2.03-2.140.1521110.12282746X-RAY DIFFRACTION100
2.14-2.270.13011460.11932674X-RAY DIFFRACTION100
2.27-2.450.14921420.12672716X-RAY DIFFRACTION100
2.45-2.690.13261470.12882737X-RAY DIFFRACTION100
2.69-3.080.15171410.14532729X-RAY DIFFRACTION100
3.08-3.880.14271440.13922772X-RAY DIFFRACTION100
3.88-45.30.1821570.15252908X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.6225 Å / Origin y: 15.9369 Å / Origin z: 21.3302 Å
111213212223313233
T0.0574 Å20.005 Å2-0.0008 Å2-0.1061 Å2-0.0021 Å2--0.0671 Å2
L0.6111 °20.1763 °20.1165 °2-1.3106 °20.2345 °2--0.5775 °2
S0.0025 Å °-0.004 Å °0.0089 Å °-0.0027 Å °-0.0008 Å °-0.0209 Å °-0.0219 Å °0.0203 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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