3FV8 | pdb_00003fv8

JNK3 bound to piperazine amide inhibitor, SR2774.

• PDB DOI: https://doi.org/10.2210/pdb3FV8/pdb

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


• Deposited: 2009-01-15 Released: 2009-04-07 
• Deposition Author(s): Habel, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Synthesis and SAR of piperazine amides as novel c-jun N-terminal kinase (JNK) inhibitors.

Shin, Y., Chen, W., Habel, J., Duckett, D., Ling, Y.Y., Koenig, M., He, Y., Vojkovsky, T., LoGrasso, P., Kamenecka, T.M.

(2009) Bioorg Med Chem Lett 19: 3344-3347

• PubMed: 19433357 
• DOI: https://doi.org/10.1016/j.bmcl.2009.03.086
• Primary Citation of Related Structures:  
  3FV8


• PubMed Abstract: 
  

  A novel series of c-jun N-terminal kinase (JNK) inhibitors were designed and developed from a high-throughput-screening hit. Through the optimization of the piperazine amide 1, several potent compounds were discovered. The X-ray crystal structure of 4g showed a unique binding mode different from other well known JNK3 inhibitors.

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Organizational Affiliation: 

Department of Molecular Therapeutics, and Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, 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: 41.74 kDa 
• Atom Count: 2,891 
• Modelled Residue Count: 334 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	355	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JK3	B [auth A]	5-bromo-N-(3-chloro-2-(4-(prop-2-ynyl)piperazin-1-yl)phenyl)furan-2-carboxamide C18 H17 Br Cl N3 O2 MEFJFXHHHNDHEN-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCY	A	L-PEPTIDE LINKING	C5 H11 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
JK3	BindingDB:  3FV8	IC50: min: 140, max: 160 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.565	α = 90
b = 125.315	β = 90
c = 69.253	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Habel, J.E.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-16
  Changes: Data collection, Source and taxonomy
• Version 2.0: 2023-09-06
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description