Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.49 kDa 
• Atom Count: 2577 
• Residue Count: 280 
• Unique protein chains: 1

2YDI

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

• DOI: 10.2210/pdb2YDI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-03-21 Released: 2012-04-04 
• Deposition Author(s): Read, J.A., Breed, J., Haye, H., McCall, E., Rowsell, S., Vallentine, A., White, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.200 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

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

• PubMed: 22551018 
• 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 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. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE CHK1	A	289	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
NIH Common Fund Data Resources
PHAROS:  O14757 GTEx:  ENSG00000149554

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YDI	A	5-[4-(2-DIMETHYLAMINOETHYLOXY)PHENYL]-2-UREIDO-THIOPHENE-3-CARBOXAMIDE C16 H20 N4 O3 S RFSVVCBVIFWEMZ-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
YDI	IC50:  150   nM  BindingDB
YDI	IC50 :  150   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.200 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.069	α = 90
b = 65.989	β = 93.79
c = 58.252	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-21 
• Released Date: 2012-04-04 
Deposition Author(s): Read, J.A., Breed, J., Haye, H., McCall, E., Rowsell, S., Vallentine, A., White, A.

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