[English] 日本語
Yorodumi
- PDB-9rf2: M. tuberculosis meets European Lead Factory: identification and s... -

+
Open data


ID or keywords:

Loading...

-
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: 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 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more