2P33

Synthesis and SAR of Aminopyrimidines as Novel c-Jun N-Terminal Kinase (JNK) Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2P33/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-08 Released: 2007-06-19 
• Deposition Author(s): Ceska, T.A., Platt, A., Fortunato, M., Dickson, K.M., Sharpe, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.304 
• R-Value Work: 0.253 

Starting Model: experimental

Literature

Synthesis and SAR of aminopyrimidines as novel c-Jun N-terminal kinase (JNK) inhibitors

Alam, M., Beevers, R.E., Ceska, T., Davenport, R.J., Dickson, K.M., Fortunato, M., Gowers, L., Haughan, A.F., James, L.A., Jones, M.W., Kinsella, N., Lowe, C., Meissner, J.W., Nicolas, A.L., Perry, B.G., Phillips, D.J., Pitt, W.R., Platt, A., Ratcliffe, A.J., Sharpe, A., Tait, L.J.

(2007) Bioorg Med Chem Lett 17: 3463-3467

• PubMed: 17459703 
• DOI: https://doi.org/10.1016/j.bmcl.2007.03.078
• Primary Citation of Related Structures:  
  2P33


• PubMed Abstract: 
  

  The development of a series of novel aminopyrimidines as inhibitors of c-Jun N-terminal kinases is described. The synthesis, in vitro inhibitory values for JNK1, JNK2 and CDK2, and the in vitro inhibitory value for a c-Jun cellular assay are discussed.

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Organizational Affiliation: 

UCB, Granta Park, Great Abington, Cambridge CB21 6GS, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.52 kDa 
• Atom Count: 2,775 
• Modelled Residue Count: 332 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
c-Jun N-terminal kinase 3	A	365	Homo sapiens	Mutation(s): 0  Gene Names: MAPK10, JNK3, JNK3A, PRKM10 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens) Explore P53779  Go to UniProtKB:  P53779
PHAROS:  P53779 GTEx:  ENSG00000109339

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J07	B [auth A]	4-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}-N-ethylpiperidine-1-carboxamide C20 H23 Cl N6 O ARMFMDYRYOKSOW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
J07	PDBBind:  2P33	IC50: 57 (nM) from 1 assay(s)
	BindingDB:  2P33	IC50: min: 13, max: 57 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.304 
• R-Value Work: 0.253 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.82	α = 90
b = 71.52	β = 90
c = 107.36	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Ceska, T.A., Platt, A., Fortunato, M., Dickson, K.M., Sharpe, A.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description