5OQ6

Structure of CHK1 12-pt. mutant complex with aminopyrimido-benzodiazepinone LRRK2 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 

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:  

  • 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 ...

    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

    Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom.,H. Lundbeck A/S , Ottiliavej 9, 2500 Valby, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase Chk1
A
297Homo sapiensMutation(s): 12 
Gene Names: CHEK1 (CHK1)
EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens)
Go to Gene View: CHEK1
Go to UniProtKB:  O14757
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
4K4
Query on 4K4

Download SDF File 
Download CCD File 
A
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4K4IC50: 82.8 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.000α = 90.00
b = 66.160β = 101.84
c = 54.980γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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