4YZM

Humanized Roco4 bound to LRRK2-In1

• PDB DOI: https://doi.org/10.2210/pdb4YZM/pdb

• Classification: TRANSFERASE
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-03-25 Released: 2015-05-06 
• Deposition Author(s): Gilsbach, B.K., Messias, A.C., Ito, G., Sattler, M., Alessi, D.R., Wittinghofer, A., Kortholt, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.196 
• R-Value Observed: 0.200 

Literature

Structural Characterization of LRRK2 Inhibitors.

Gilsbach, B.K., Messias, A.C., Ito, G., Sattler, M., Alessi, D.R., Wittinghofer, A., Kortholt, A.

(2015) J Med Chem 58: 3751-3756

• PubMed: 25897865 
• DOI: https://doi.org/10.1021/jm5018779
• Primary Citation of Related Structures:  
  4YZM, 4YZN


• PubMed Abstract: 
  

  Kinase inhibition is considered to be an important therapeutic target for LRRK2 mediated Parkinson's disease (PD). Many LRRK2 kinase inhibitors have been reported but have yet to be optimized in order to qualify as drug candidates for the treatment of the disease. In order to start a structure-function analysis of such inhibitors, we mutated the active site of Dictyostelium Roco4 kinase to resemble LRRK2. Here, we show saturation transfer difference (STD) NMR and the first cocrystal structures of two potent in vitro inhibitors, LRRK2-IN-1 and compound 19, with mutated Roco4. Our data demonstrate that this system can serve as an excellent tool for the structural characterization and optimization of LRRK2 inhibitors using X-ray crystallography and NMR spectroscopy.

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Organizational Affiliation: 

†Department of Cell Biochemistry, University of Groningen, 9747AG Groningen, The Netherlands.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.29 kDa 
• Atom Count: 4,330 
• Modelled Residue Count: 522 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable serine/threonine-protein kinase roco4	A, B	287	Dictyostelium discoideum	Mutation(s): 2  Gene Names: roco4, DDB_G0288251 EC: 2.7.11.1
UniProt
Find proteins for Q6XHB2 (Dictyostelium discoideum) Explore Q6XHB2  Go to UniProtKB:  Q6XHB2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4K4	C [auth A], E [auth B]	2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one C31 H38 N8 O3 IWMCPJZTADUIFX-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.196 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.03	α = 90
b = 89.07	β = 90
c = 177.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Gilsbach, B.K., Messias, A.C., Ito, G., Sattler, M., Alessi, D.R., Wittinghofer, A., Kortholt, A.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2015-05-27
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description