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- PDB-9rf2: M. tuberculosis meets European Lead Factory: identification and s... -

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Basic information

Entry
Database: PDB / ID: 9rf2
TitleM. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography: ELF5
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
: / : / Monoacylglycerol lipase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRiegler-Berket, L. / Goedl, L. / Oberer, M. / Polidori, N.
Funding support Austria, 3items
OrganizationGrant numberCountry
Austrian Science FundF73 Austria
Austrian Science FundDOC 50 Austria
Austrian Science FundDOC 130 Austria
CitationJournal: To Be Published
Title: M. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography
Authors: Riegler-Berket, L. / Goedl, L. / Oberer, M. / Polidori, N.
History
DepositionJun 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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)34,4144
Polymers33,6181
Non-polymers7963
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.411, 82.784, 90.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Monoacylglycerol lipase / MGL


Mass: 33618.047 Da / Num. of mol.: 1 / Mutation: K74A
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
#2: Chemical ChemComp-8KE / [1-[6-[(4-methoxyphenyl)amino]pyrimidin-4-yl]pyrazol-4-yl]-[(3S)-3-oxidanylpyrrolidin-1-yl]methanone


Mass: 380.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-I3F / [1-[6-[(4-methoxyphenyl)amino]pyrimidin-4-yl]pyrazol-4-yl]-[(3R)-3-oxidanylpyrrolidin-1-yl]methanone


Mass: 380.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N6O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
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: 1.03323 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.6→41.39 Å / Num. obs: 40806 / % possible obs: 99.49 % / Redundancy: 2 % / Biso Wilson estimate: 30.94 Å2 / CC1/2: 1 / Net I/σ(I): 17.54
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 3911 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→41.39 Å / SU ML: 0.1909 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7944 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 1989 4.88 %
Rwork0.19 --
obs0.1902 40788 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.84 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 29 62 2213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052335
X-RAY DIFFRACTIONf_angle_d0.8583204
X-RAY DIFFRACTIONf_dihedral_angle_d12.909907
X-RAY DIFFRACTIONf_chiral_restr0.057359
X-RAY DIFFRACTIONf_plane_restr0.009425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.34571300.322627X-RAY DIFFRACTION96
1.64-1.680.30031290.27122758X-RAY DIFFRACTION99
1.68-1.730.28541410.24432716X-RAY DIFFRACTION100
1.73-1.790.24221420.23772720X-RAY DIFFRACTION100
1.79-1.850.26421410.21572772X-RAY DIFFRACTION100
1.85-1.930.23941410.20362781X-RAY DIFFRACTION100
1.93-2.020.19591500.1852743X-RAY DIFFRACTION100
2.02-2.120.2271380.17812761X-RAY DIFFRACTION100
2.12-2.260.21351230.17722769X-RAY DIFFRACTION100
2.26-2.430.21851400.17832776X-RAY DIFFRACTION100
2.43-2.670.20561710.17672772X-RAY DIFFRACTION100
2.67-3.060.21671360.19022802X-RAY DIFFRACTION100
3.06-3.860.18881530.1722825X-RAY DIFFRACTION100
3.86-41.390.17061540.19142978X-RAY DIFFRACTION99

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