5F4N | pdb_00005f4n

Multi-parameter lead optimization to give an oral CHK1 inhibitor clinical candidate: (R)-5-((4-((morpholin-2-ylmethyl)amino)-5-(trifluoromethyl)pyridin-2-yl)amino)pyrazine-2-carbonitrile (CCT245737)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.188 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5F4N

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Multiparameter Lead Optimization to Give an Oral Checkpoint Kinase 1 (CHK1) Inhibitor Clinical Candidate: (R)-5-((4-((Morpholin-2-ylmethyl)amino)-5-(trifluoromethyl)pyridin-2-yl)amino)pyrazine-2-carbonitrile (CCT245737).

Osborne, J.D.Matthews, T.P.McHardy, T.Proisy, N.Cheung, K.M.Lainchbury, M.Brown, N.Walton, M.I.Eve, P.D.Boxall, K.J.Hayes, A.Henley, A.T.Valenti, M.R.De Haven Brandon, A.K.Box, G.Jamin, Y.Robinson, S.P.Westwood, I.M.van Montfort, R.L.Leonard, P.M.Lamers, M.B.Reader, J.C.Aherne, G.W.Raynaud, F.I.Eccles, S.A.Garrett, M.D.Collins, I.

(2016) J Med Chem 59: 5221-5237

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01938
  • Primary Citation Related Structures: 
    5F4N

  • PubMed Abstract: 

    Multiparameter optimization of a series of 5-((4-aminopyridin-2-yl)amino)pyrazine-2-carbonitriles resulted in the identification of a potent and selective oral CHK1 preclinical development candidate with in vivo efficacy as a potentiator of deoxyribonucleic acid (DNA) damaging chemotherapy and as a single agent. Cellular mechanism of action assays were used to give an integrated assessment of compound selectivity during optimization resulting in a highly CHK1 selective adenosine triphosphate (ATP) competitive inhibitor. A single substituent vector directed away from the CHK1 kinase active site was unexpectedly found to drive the selective cellular efficacy of the compounds. Both CHK1 potency and off-target human ether-a-go-go-related gene (hERG) ion channel inhibition were dependent on lipophilicity and basicity in this series. Optimization of CHK1 cellular potency and in vivo pharmacokinetic-pharmacodynamic (PK-PD) properties gave a compound with low predicted doses and exposures in humans which mitigated the residual weak in vitro hERG inhibition.


  • Organizational Affiliation
    • Sareum Ltd. , Cambridge CB22 3FX, U.K.

Macromolecule Content 

  • Total Structure Weight: 32.63 kDa 
  • Atom Count: 2,450 
  • Modeled Residue Count: 258 
  • Deposited Residue Count: 273 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1273Homo sapiensMutation(s): 0 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5UY

Query on 5UY



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
methyl 6-[(5-cyanopyrazin-2-yl)amino]-4-[[(2~{R})-morpholin-2-yl]methylamino]pyridine-3-carboxylate
C17 H19 N7 O3
PHPWNBVMNTWSJB-GFCCVEGCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.188 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.97α = 90
b = 65.87β = 94.69
c = 57.9γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references