3PTG

Design and Synthesis of a Novel, Orally Efficacious Tri-substituted Thiophene Based JNK Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3PTG/pdb

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


• Deposited: 2010-12-02 Released: 2011-03-02 
• Deposition Author(s): Bowers, S., Truong, A.P., Neitz, J., Neitzel, M., Probst, G.D., Hom, R.K., Konradi, A.W., Sham, H.L., Toth, G., Pan, H., Yao, N., Artis, D.R., Brigham, E.F., Quinn, K.P., Sauer, J., Powell, K., Ruslim, L., Bard, F., Yednock, T.A., Griswold-Prenner, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.316 
• R-Value Work: 0.244 
• R-Value Observed: 0.247 

Literature

Design and synthesis of a novel, orally active, brain penetrant, tri-substituted thiophene based JNK inhibitor.

Bowers, S., Truong, A.P., Neitz, R.J., Neitzel, M., Probst, G.D., Hom, R.K., Peterson, B., Galemmo, R.A., Konradi, A.W., Sham, H.L., Toth, G., Pan, H., Yao, N., Artis, D.R., Brigham, E.F., Quinn, K.P., Sauer, J.M., Powell, K., Ruslim, L., Ren, Z., Bard, F., Yednock, T.A., Griswold-Prenner, I.

(2011) Bioorg Med Chem Lett 21: 1838-1843

• PubMed: 21316234 
• DOI: https://doi.org/10.1016/j.bmcl.2011.01.046
• Primary Citation of Related Structures:  
  3PTG


• PubMed Abstract: 
  

  The SAR of a series of tri-substituted thiophene JNK3 inhibitors is described. By optimizing both the N-aryl acetamide region of the inhibitor and the 4-position of the thiophene we obtained single digit nanomolar compounds, such as 47, which demonstrated an in vivo effect on JNK activity when dosed orally in our kainic acid mouse model as measured by phospho-c-jun reduction.

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Organizational Affiliation: 

Department of Chemical Sciences, Elan Pharmaceuticals, South San Francisco, CA 94080, USA. [e-mail]

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: 43.58 kDa 
• Atom Count: 2,895 
• Modelled Residue Count: 350 
• Deposited Residue Count: 374 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	363	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-Jun-amino-terminal kinase-interacting protein 1	B [auth J]	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
932	C [auth A]	N-[4-methyl-3-(1H-1,2,4-triazol-5-yl)thiophen-2-yl]-2-(2-oxo-3,4-dihydroquinolin-1(2H)-yl)acetamide C18 H17 N5 O2 S HJUDFJRTVGXBRF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
932	BindingDB:  3PTG	IC50: min: 100, max: 5050 (nM) from 3 assay(s)
	PDBBind:  3PTG	IC50: 25 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.316 
• R-Value Work: 0.244 
• R-Value Observed: 0.247 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.772	α = 90
b = 80.434	β = 90
c = 83.45	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-02 
Deposition Author(s): Bowers, S., Truong, A.P., Neitz, J., Neitzel, M., Probst, G.D., Hom, R.K., Konradi, A.W., Sham, H.L., Toth, G., Pan, H., Yao, N., Artis, D.R., Brigham, E.F., Quinn, K.P., Sauer, J., Powell, K., Ruslim, L., Bard, F., Yednock, T.A., Griswold-Prenner, I.

Revision History  

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations