5OP4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.7b01186
  • Primary Citation of Related Structures:  
    5OOP, 5OOR, 5OOT, 5OP2, 5OP4, 5OP5, 5OP7, 5OPB, 5OPR, 5OPS, 5OPU, 5OPV, 5OQ5, 5OQ6, 5OQ7, 5OQ8

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1297Homo sapiensMutation(s): 10 
Gene Names: CHEK1CHK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
PHAROS:  O14757
GTEx:  ENSG00000149554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A0T (Subject of Investigation/LOI)
Query on A0T

Download Ideal Coordinates CCD File 
B [auth A][4-[[4-(ethylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-fluoranyl-5-methoxy-phenyl]-morpholin-4-yl-methanone
C19 H21 F4 N5 O3
XCFLWTZSJYBCPF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.25α = 90
b = 66.21β = 102.23
c = 54.61γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A0TClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description