7BJX

Crystal structure of CHK1-10pt-mutant complex with compound 26


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design and Synthesis of Pyrrolo[2,3- d ]pyrimidine-Derived Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Checkpoint Kinase 1 (CHK1)-Derived Crystallographic Surrogate.

Williamson, D.S.Smith, G.P.Mikkelsen, G.K.Jensen, T.Acheson-Dossang, P.Badolo, L.Bedford, S.T.Chell, V.Chen, I.J.Dokurno, P.Hentzer, M.Newland, S.Ray, S.C.Shaw, T.Surgenor, A.E.Terry, L.Wang, Y.Christensen, K.V.

(2021) J Med Chem 64: 10312-10332

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00720
  • Primary Citation of Related Structures:  
    7BJD, 7BJE, 7BJH, 7BJJ, 7BJM, 7BJO, 7BJR, 7BJX, 7BK1, 7BK2, 7BK3, 7BKN, 7BKO

  • PubMed Abstract: 

    Inhibitors of leucine-rich repeat kinase 2 (LRRK2) and mutants, such as G2019S, have potential utility in Parkinson's disease treatment. Fragment hit-derived pyrrolo[2,3- d ]pyrimidines underwent optimization using X-ray structures of LRRK2 kinase domain surrogates, based on checkpoint kinase 1 (CHK1) and a CHK1 10-point mutant. (2 R )-2-Methylpyrrolidin-1-yl derivative 18 (LRRK2 G2019S c K i 0.7 nM, LE 0.66) was identified, with increased potency consistent with an X-ray structure of 18 /CHK1 10-pt. mutant showing the 2-methyl substituent proximal to Ala147 (Ala2016 in LRRK2). Further structure-guided elaboration of 18 gave the 2-[(1,3-dimethyl-1 H -pyrazol-4-yl)amino] derivative 32 . Optimization of 32 afforded diastereomeric oxolan-3-yl derivatives 44 and 45 , which demonstrated a favorable in vitro PK profile, although they displayed species disconnects in the in vivo PK profile, and a propensity for P-gp- and/or BCRP-mediated efflux in a mouse model. Compounds 44 and 45 demonstrated high potency and exquisite selectivity for LRRK2 and utility as chemical probes for the study of LRRK2 inhibition.


  • Organizational Affiliation

    Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1
A, B
297Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U0Q (Subject of Investigation/LOI)
Query on U0Q

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-amino-7-methyl-2-[(1-methyl-1H-pyrazol-4-yl)amino]-6-[(2R)-2-methylpyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
C17 H21 N9
QQIQPTYOVZSTDB-SNVBAGLBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.993α = 90
b = 65.942β = 101.32
c = 110.057γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Derived calculations
  • Version 1.2: 2021-08-04
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description