4L7F

Co-crystal Structure of JNK1 and AX13587

• PDB DOI: https://doi.org/10.2210/pdb4L7F/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2013-06-13 Released: 2013-08-21 
• Deposition Author(s): Walter, R.L., Ranieri, G.M., Riggs, A.M., Weissig, H., Li, B., Shreder, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Hit-to-lead optimization and kinase selectivity of imidazo[1,2-a]quinoxalin-4-amine derived JNK1 inhibitors.

Li, B., Cociorva, O.M., Nomanbhoy, T., Weissig, H., Li, Q., Nakamura, K., Liyanage, M., Zhang, M.C., Shih, A.Y., Aban, A., Hu, Y., Cajica, J., Pham, L., Kozarich, J.W., Shreder, K.R.

(2013) Bioorg Med Chem Lett 23: 5217-5222

• PubMed: 23916259 
• DOI: https://doi.org/10.1016/j.bmcl.2013.06.087
• Primary Citation of Related Structures:  
  4L7F


• PubMed Abstract: 
  

  As the result of a rhJNK1 HTS, the imidazo[1,2-a]quinoxaline 1 was identified as a 1.6 μM rhJNK1 inhibitor. Optimization of this compound lead to AX13587 (rhJNK1 IC50=160 nM) which was co-crystallized with JNK1 to identify key molecular interactions. Kinase profiling against 125+ kinases revealed AX13587 was an inhibitor of JNK, MAST3, and MAST4 whereas its methylene homolog AX14373 (native JNK1 IC50=47 nM) was a highly specific JNK inhibitor.

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Organizational Affiliation: 

ActivX Biosciences, Inc., 11025 N. Torrey Pines Road, La Jolla, CA 92037, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 42.84 kDa 
• Atom Count: 3,554 
• Modelled Residue Count: 354 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 8	A	367	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1V5	B [auth A]	N-[1-(4-fluorophenyl)cyclopropyl]-4-[(trans-4-hydroxycyclohexyl)amino]imidazo[1,2-a]quinoxaline-8-carboxamide C26 H26 F N5 O2 MFJOWCFANZXQBU-MXVIHJGJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.802	α = 90
b = 135.802	β = 90
c = 94.208	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Walter, R.L., Ranieri, G.M., Riggs, A.M., Weissig, H., Li, B., Shreder, K.R.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations