4E73 | pdb_00004e73

Crystal structure of JNK1beta-JIP in complex with an azaquinolone inhbitor

• PDB DOI: https://doi.org/10.2210/pdb4E73/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-16 Released: 2013-05-29 
• Deposition Author(s): Lukacs, C.M., Janson, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.282 (Depositor) 
• R-Value Work: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Identification of an Adamantyl Azaquinolone JNK Selective Inhibitor.

Haynes, N.E., Scott, N.R., Chen, L.C., Janson, C.A., Li, J.K., Lukacs, C.M., Railkar, A., Tozzo, E., Whittard, T., Brown, N.F., Cheung, A.W.

(2012) ACS Med Chem Lett 3: 764-768

• PubMed: 24900545 
• DOI: https://doi.org/10.1021/ml300175c
• Primary Citation Related Structures: 
  4E73


• PubMed Abstract: 
  

  3-[4-((1S,2S,3R,5S,7S)-5-Hydroxyadamantan-2-ylcarbamoyl)benzyl]-4-oxo-1-phenyl-1,4-dihydro-[1,8]naphthyridine-2-carboxylic acid methyl ester (4) was identified as a novel, druglike and selective quinolone pan JNK inhibitor. In this communication, some of the structure-activity relationship of the azaquinolone analogues leading to 4 is discussed. The focus is on how changes at the amide functionality affected the biochemical potency, cellular potency, metabolic properties, and solubility of this class of JNK inhibitors. Optimization of these properties led to the identification of the adamantyl analogue, 4. 4 achieved proof of mechanism in both rat and mouse TNF-α challenge models.

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Organizational Affiliation: 
• Hoffmann-La Roche Inc. , pRED, Pharma Research & Early Development, DTA Metabolism, 340 Kingsland Street, Nutley, New Jersey 07110, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 44.47 kDa 
• Atom Count: 2,784 
• Modeled Residue Count: 327 
• Deposited Residue Count: 380 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 8	A	369	Homo sapiens	Mutation(s): 0  Gene Names: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens) Explore P45983  Go to UniProtKB:  P45983
PHAROS:  P45983 GTEx:  ENSG00000107643

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-Jun-amino-terminal kinase-interacting protein 1	B	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQF2 (Homo sapiens) Explore Q9UQF2  Go to UniProtKB:  Q9UQF2
PHAROS:  Q9UQF2 GTEx:  ENSG00000121653

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0NR	C [auth A]	methyl 3-(4-{[(1R,2S,3S,5S,7s)-5-aminotricyclo[3.3.1.1~3,7~]dec-2-yl]carbamoyl}benzyl)-4-oxo-1-phenyl-1,4-dihydro-1,8-naphthyridine-2-carboxylate C34 H34 N4 O4 OVPCOPWFTZDTCI-CJYKQNLHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.282 (Depositor) 
• R-Value Work:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.901	α = 90
b = 79.84	β = 90
c = 85.524	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Lukacs, C.M., Janson, C.A.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description