2O0U

Crystal structure of human JNK3 complexed with N-{3-cyano-6-[3-(1-piperidinyl)propanoyl]-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl}-1-naphthalenecarboxamide

• PDB DOI: https://doi.org/10.2210/pdb2O0U/pdb

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


• Deposited: 2006-11-28 Released: 2007-02-27 
• Deposition Author(s): Rowland, P., Somers, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.283 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

N-(3-Cyano-4,5,6,7-tetrahydro-1-benzothien-2-yl)amides as potent, selective, inhibitors of JNK2 and JNK3.

Angell, R.M., Atkinson, F.L., Brown, M.J., Chuang, T.T., Christopher, J.A., Cichy-Knight, M., Dunn, A.K., Hightower, K.E., Malkakorpi, S., Musgrave, J.R., Neu, M., Rowland, P., Shea, R.L., Smith, J.L., Somers, D.O., Thomas, S.A., Thompson, G., Wang, R.

(2007) Bioorg Med Chem Lett 17: 1296-1301

• PubMed: 17194588 
• DOI: https://doi.org/10.1016/j.bmcl.2006.12.003
• Primary Citation of Related Structures:  
  2O0U, 2O2U


• PubMed Abstract: 
  

  The identification and exploration of a novel, potent and selective series of N-(3-cyano-4,5,6,7-tetrahydro-1-benzothien-2-yl)amide inhibitors of JNK2 and JNK3 kinases is described. Compounds 5a and 11a were identified as potent inhibitors of JNK3 (pIC50 6.7 and 6.6, respectively), with essentially equal potency against JNK2 (pIC50 6.5). Selectivity within the mitogen-activated protein kinase (MAPK) family, against JNK1, p38alpha and ERK2, was observed for the series. X-ray crystallography of 5e and 8a in JNK3 revealed a unique binding mode, with the 3-cyano substituent forming an H-bond acceptor interaction with the hinge region of the ATP-binding site.

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Organizational Affiliation: 

GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.53 kDa 
• Atom Count: 2,899 
• Modelled Residue Count: 331 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	364	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
C0M	B [auth A]	N-{3-CYANO-6-[3-(1-PIPERIDINYL)PROPANOYL]-4,5,6,7-TETRAHYDROTHIENO[2,3-C]PYRIDIN-2-YL}1-NAPHTHALENECARBOXAMIDE C27 H28 N4 O2 S PRZGSWGFNRYBIP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C0M	PDBBind:  2O0U	Ki: 3200 (nM) from 1 assay(s)
	BindingDB:  2O0U	IC50: min: 3162.28, max: 1.00e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.283 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.793	α = 90
b = 71.653	β = 90
c = 107.857	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Rowland, P., Somers, D.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations