3RTP

Design and synthesis of brain penetrant selective JNK inhibitors with improved pharmacokinetic properties for the prevention of neurodegeneration

• PDB DOI: https://doi.org/10.2210/pdb3RTP/pdb

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


• Deposited: 2011-05-03 Released: 2013-05-08 
• Deposition Author(s): Bowers, S., Truong, A.P., Neitz, R.J., Hom, R.K., Sealy, J.M., Probst, G.D., Quincy, Q., Peterson, B., Chan, W., Galemmo Jr., R.A., Konradi, A.W., Sham, H.L., Pan, H., Lin, M., Yao, N., Artis, D.R., Zhang, H., Chen, L., Dryer, M., Samant, B., Zmolek, W., Wong, K., Lorentzen, C., Goldbach, E., Tonn, G., Quinn, K.P., Sauer, J., Wright, S., Powell, K., Ruslim, L., Ren, Z., Bard, F., Yednock, T.A., Griswold-Prenne, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.309 
• R-Value Work: 0.235 
• R-Value Observed: 0.240 

Literature

Design and synthesis of brain penetrant selective JNK inhibitors with improved pharmacokinetic properties for the prevention of neurodegeneration.

Bowers, S., Truong, A.P., Jeffrey Neitz, R., Hom, R.K., Sealy, J.M., Probst, G.D., Quincy, D., Peterson, B., Chan, W., Galemmo, R.A., Konradi, A.W., Sham, H.L., Toth, G., Pan, H., Lin, M., Yao, N., Artis, D.R., Zhang, H., Chen, L., Dryer, M., Samant, B., Zmolek, W., Wong, K., Lorentzen, C., Goldbach, E., Tonn, G., Quinn, K.P., Sauer, J.M., Wright, S., Powell, K., Ruslim, L., Ren, Z., Bard, F., Yednock, T.A., Griswold-Prenner, I.

(2011) Bioorg Med Chem Lett 21: 5521-5527

• PubMed: 21813278 
• DOI: https://doi.org/10.1016/j.bmcl.2011.06.100
• Primary Citation of Related Structures:  
  3RTP


• PubMed Abstract: 
  

  The SAR of a series of brain penetrant, trisubstituted thiophene based JNK inhibitors with improved pharmacokinetic properties is described. These compounds were designed based on information derived from metabolite identification studies which led to compounds such as 42 with lower clearance, greater brain exposure and longer half life compared to earlier analogs.

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Organizational Affiliation: 

Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, United States. [e-mail]

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: 42.25 kDa 
• Atom Count: 2,735 
• Modelled Residue Count: 331 
• Deposited Residue Count: 363 
• Unique protein chains: 1

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
34I	B [auth A]	N-[4-cyano-3-(1H-1,2,4-triazol-5-yl)thiophen-2-yl]-2-(2-oxo-3,4-dihydroquinolin-1(2H)-yl)acetamide C18 H14 N6 O2 S WNRCGOJLZOLSJN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
34I	BindingDB:  3RTP	IC50: min: 100, max: 100 (nM) from 3 assay(s)
	PDBBind:  3RTP	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.309 
• R-Value Work: 0.235 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.297	α = 90
b = 71.701	β = 90
c = 108.302	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Bowers, S., Truong, A.P., Neitz, R.J., Hom, R.K., Sealy, J.M., Probst, G.D., Quincy, Q., Peterson, B., Chan, W., Galemmo Jr., R.A., Konradi, A.W., Sham, H.L., Pan, H., Lin, M., Yao, N., Artis, D.R., Zhang, H., Chen, L., Dryer, M., Samant, B., Zmolek, W., Wong, K., Lorentzen, C., Goldbach, E., Tonn, G., Quinn, K.P., Sauer, J., Wright, S., Powell, K., Ruslim, L., Ren, Z., Bard, F., Yednock, T.A., Griswold-Prenne, I.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations