2YDK

Discovery of Checkpoint Kinase Inhibitor AZD7762 by Structure Based Design and Optimization of Thiophene Carboxamide Ureas


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery of Checkpoint Kinase Inhibitor (S)-5-(3-Fluorophenyl)-N-(Piperidin-3-Yl)-3-Ureidothiophene-2-Carboxamide (Azd7762) by Structure-Based Design and Optimization of Thiophenecarboxamide Ureas.

Oza, V.Ashwell, S.Almeida, L.Brassil, P.Breed, J.Deng, C.Gero, T.Grondine, M.Horn, C.Ioannidis, S.Liu, D.Lyne, P.Newcombe, N.Pass, M.Read, J.A.Ready, S.Rowsell, S.Su, M.Toader, D.Vasbinder, M.Yu, D.Yu, Y.Xue, Y.Zabludoff, S.Janetka, J.

(2012) J Med Chem 55: 5130

  • DOI: 10.1021/jm300025r
  • Primary Citation of Related Structures:  
    2YDI, 2YDJ, 2YDK, 3PZE

  • PubMed Abstract: 
  • Checkpoint kinases CHK1 and CHK2 are activated in response to DNA damage that results in cell cycle arrest, allowing sufficient time for DNA repair. Agents that lead to abrogation of such checkpoints have potential to increase the efficacy of such co ...

    Checkpoint kinases CHK1 and CHK2 are activated in response to DNA damage that results in cell cycle arrest, allowing sufficient time for DNA repair. Agents that lead to abrogation of such checkpoints have potential to increase the efficacy of such compounds as chemo- and radiotherapies. Thiophenecarboxamide ureas (TCUs) were identified as inhibitors of CHK1 by high throughput screening. A structure-based approach is described using crystal structures of JNK1 and CHK1 in complex with 1 and 2 and of the CHK1-3b complex. The ribose binding pocket of CHK1 was targeted to generate inhibitors with excellent cellular potency and selectivity over CDK1and IKKβ, key features lacking from the initial compounds. Optimization of 3b resulted in the identification of a regioisomeric 3-TCU lead 12a. Optimization of 12a led to the discovery of the clinical candidate 4 (AZD7762), which strongly potentiates the efficacy of a variety of DNA-damaging agents in preclinical models.


    Organizational Affiliation

    AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States. vibha.oza@gmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE CHK1A276Homo sapiensMutation(s): 0 
Gene Names: CHEK1CHK1
EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
NIH Common Fund Data Resources
PHAROS  O14757
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YDK
Query on YDK

Download CCD File 
A
2-(CARBAMOYLAMINO)-5-PHENYL-N-[(3S)-PIPERIDIN-3-YL]THIOPHENE-3-CARBOXAMIDE
C17 H20 N4 O2 S
UXZRCIBKIDILEF-LBPRGKRZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YDKIC50:  7   nM  BindingDB
YDKIC50:  7   nM  Binding MOAD
YDKEC50:  450   nM  BindingDB
YDKEC50:  19   nM  BindingDB
YDKEC50:  20   nM  BindingDB
YDKIC50 :  7   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.613α = 90
b = 70.791β = 90
c = 104.063γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-06-27
    Changes: Other
  • Version 1.2: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.3: 2019-10-09
    Changes: Data collection, Other