3G9N | pdb_00003g9n

JNK3 bound to (Z)-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl)-3-(hydroxyimino)-4-phenylindolin-2-one

• PDB DOI: https://doi.org/10.2210/pdb3G9N/pdb

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


• Deposited: 2009-02-13 Released: 2009-02-24 
• Deposition Author(s): Jacobs, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.326 (Depositor), 0.328 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structure-based design and parallel synthesis of N-benzyl isatin oximes as JNK3 MAP kinase inhibitors.

Cao, J., Gao, H., Bemis, G., Salituro, F., Ledeboer, M., Harrington, E., Wilke, S., Taslimi, P., Pazhanisamy, S., Xie, X., Jacobs, M., Green, J.

(2009) Bioorg Med Chem Lett 19: 2891-2895

• PubMed: 19361991 
• DOI: https://doi.org/10.1016/j.bmcl.2009.03.043
• Primary Citation Related Structures: 
  3G90, 3G9L, 3G9N


• PubMed Abstract: 
  

  A series of N-benzylated isatin oximes were developed as inhibitors of the mitogen-activated kinase, JNK3. X-ray crystallographic structures aided in the design and synthesis of novel, selective compounds, that inhibit JNK3, but not p38 MAP kinase and provided key insights into understanding the behavior of gatekeeper residue methionine-146 in determining target selectivity for this series.

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Organizational Affiliation: 
• Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139, United States.

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: 42.52 kDa 
• Atom Count: 2,841 
• Modeled Residue Count: 346 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	365	Homo sapiens	Mutation(s): 0  Gene Names: JNK3, JNK3A, MAPK10, 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
J88	B [auth A]	(3Z)-1-[(6-fluoro-4H-1,3-benzodioxin-8-yl)methyl]-4-phenyl-1H-indole-2,3-dione 3-oxime C23 H17 F N2 O4 SZYREAUDQRVVLV-DAFNUICNSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
J88	BindingDB:  3G9N	Ki: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.326 (Depositor), 0.328 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.313	α = 90
b = 72.176	β = 90
c = 107.489	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): Jacobs, M.D.

Revision History  

• Version 1.0: 2009-02-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations