9RF2 | pdb_00009rf2

M. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography: ELF5

• PDB DOI: https://doi.org/10.2210/pdb9RF2/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-06-04 Released: 2025-08-13 
• Deposition Author(s): Riegler-Berket, L., Goedl, L., Oberer, M., Polidori, N.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

M. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography

Riegler-Berket, L., Goedl, L., Oberer, M., Polidori, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.41 kDa 
• Atom Count: 2,336 
• Modeled Residue Count: 278 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoacylglycerol lipase	A	307	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: Rv0183 EC: 3.1.1.23
UniProt
Find proteins for O07427 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O07427  Go to UniProtKB:  O07427

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I3F	C [auth A]	[1-[6-[(4-methoxyphenyl)amino]pyrimidin-4-yl]pyrazol-4-yl]-[(3R)-3-oxidanylpyrrolidin-1-yl]methanone C19 H20 N6 O3 XCPMHUGYOPFVKI-OAHLLOKOSA-N
8KE (Subject of Investigation/LOI)	B [auth A]	[1-[6-[(4-methoxyphenyl)amino]pyrimidin-4-yl]pyrazol-4-yl]-[(3S)-3-oxidanylpyrrolidin-1-yl]methanone C19 H20 N6 O3 XCPMHUGYOPFVKI-HNNXBMFYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.411	α = 90
b = 82.784	β = 90
c = 90.704	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Riegler-Berket, L., Goedl, L., Oberer, M., Polidori, N.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	F73
Austrian Science Fund	Austria	DOC 50
Austrian Science Fund	Austria	DOC 130

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release