5OP7

Structure of CHK1 10-pt. mutant complex with pyrrolopyrimidine LRRK2 inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Design of Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Crystallographic Surrogate Derived from Checkpoint Kinase 1 (CHK1).

Williamson, D.S., Smith, G.P., Acheson-Dossang, P., Bedford, S.T., Chell, V., Chen, I.J., Daechsel, J.C.A., Daniels, Z., David, L., Dokurno, P., Hentzer, M., Herzig, M.C., Hubbard, R.E., Moore, J.D., Murray, J.B., Newland, S., Ray, S.C., Shaw, T., Surgenor, A.E., Terry, L., Thirstrup, K., Wang, Y., Christensen, K.V.

(2017) J Med Chem 60: 8945-8962

  • DOI: 10.1021/acs.jmedchem.7b01186
  • Primary Citation of Related Structures:  
    5OOP, 5OOR, 5OP2, 5OOT, 5OP5, 5OP4, 5OPS, 5OPR, 5OPU, 5OQ6

  • PubMed Abstract: 

    • Mutations in leucine-rich repeat kinase 2 (LRRK2), such as G2019S, are associated with an increased risk of developing Parkinson's disease. Surrogates for the LRRK2 kinase domain based on checkpoint kinase 1 (CHK1) mutants were designed, expressed in ins ...

    Mutations in leucine-rich repeat kinase 2 (LRRK2), such as G2019S, are associated with an increased risk of developing Parkinson's disease. Surrogates for the LRRK2 kinase domain based on checkpoint kinase 1 (CHK1) mutants were designed, expressed in insect cells infected with baculovirus, purified, and crystallized. X-ray structures of the surrogates complexed with known LRRK2 inhibitors rationalized compound potency and selectivity. The CHK1 10-point mutant was preferred, following assessment of surrogate binding affinity with LRRK2 inhibitors. Fragment hit-derived arylpyrrolo[2,3-b]pyridine LRRK2 inhibitors underwent structure-guided optimization using this crystallographic surrogate. LRRK2-pSer935 HEK293 IC 50 data for 22 were consistent with binding to Ala2016 in LRRK2 (equivalent to Ala147 in CHK1 10-point mutant structure). Compound 22 was shown to be potent, moderately selective, orally available, and brain-penetrant in wild-type mice, and confirmation of target engagement was demonstrated, with LRRK2-pSer935 IC 50 values for 22 in mouse brain and kidney being 1.3 and 5 nM, respectively.

    Organizational Affiliation: 

    H. Lundbeck A/S , Ottiliavej 9, 2500 Valby, Denmark.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1 A297Homo sapiensMutation(s): 10 
Gene Names: CHEK1, CHK1
EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
NIH Common Fund Data Resources
PHAROS:  O14757
GTEx:  ENSG00000149554
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A1K
Query on A1K
Download Ideal Coordinates CCD File 
A
[4-[[5-chloranyl-4-(methylamino)-7~{H}-pyrrolo[2,3-d]pyrimidin-2-yl]amino]-3-methoxy-phenyl]-morpholin-4-yl-methanone
C19 H21 Cl N6 O3
HUEKBQXFNHWTQQ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.07α = 90
b = 65.62β = 101.99
c = 54.37γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references