Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 44403.40 
• Atom Count: 2707 
• Residue Count: 380 
• Unique protein chains: 2

4IZY

Crystal structure of JNK1 in complex with JIP1 peptide and 4-{4-[4-(4-Methanesulfonyl-piperidin-1-yl)-indol-1-yl]-pyrimidin-2-ylamino}-cyclohexan

• DOI: 10.2210/pdb4IZY/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-01-30 Released: 2013-12-18 
• Deposition Author(s): Kuglstatter, A., Shao, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.261 
• R-Value Work: 0.238 

Literature

Development of indole/indazole-aminopyrimidines as inhibitors of c-Jun N-terminal kinase (JNK): optimization for JNK potency and physicochemical properties.

Gong, L., Han, X., Silva, T., Tan, Y.C., Goyal, B., Tivitmahaisoon, P., Trejo, A., Palmer, W., Hogg, H., Jahagir, A., Alam, M., Wagner, P., Stein, K., Filonova, L., Loe, B., Makra, F., Rotstein, D., Rapatova, L., Dunn, J., Zuo, F., Dal Porto, J., Wong, B., Jin, S., Chang, A., Tran, P., Hsieh, G., Niu, L., Shao, A., Reuter, D., Hermann, J., Kuglstatter, A., Goldstein, D.

(2013) Bioorg.Med.Chem.Lett. 23: 3565-3569

• PubMed: 23664880 
• DOI: 10.1016/j.bmcl.2013.04.029


• PubMed Abstract: 
  

A novel series of indole/indazole-aminopyrimidines was designed and synthesized with an aim to achieve optimal potency and selectivity for the c-Jun kinase family or JNKs. Structure guided design was used to optimize the series resulting in a significant potency improvement. The best compound (17) has IC50 of 3 nM for JNK1 and 20 nM for JNK2, with greater than 40-fold selectivity against other kinases with good physicochemical and pharmacokinetic properties.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Roche Palo Alto, Palo Alto, CA 94304, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mitogen-activated protein kinase 8	A	369	Homo sapiens	Mutation(s): 0  Gene Names: MAPK8 (JNK1, PRKM8, SAPK1, SAPK1C) EC: 2.7.11.24
Find proteins for P45983 (Homo sapiens) Go to Gene View: MAPK8 Go to UniProtKB:  P45983

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
C-Jun-amino-terminal kinase-interacting protein 1	B	11	Homo sapiens	Mutation(s): 0  Gene Names: MAPK8IP1 (IB1, JIP1, PRKM8IP)
Find proteins for Q9UQF2 (Homo sapiens) Go to Gene View: MAPK8IP1 Go to UniProtKB:  Q9UQF2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
1J2	A	trans-4-[(4-{4-[4-(methylsulfonyl)piperidin-1-yl]-1H-indol-1-yl}pyrimidin-2-yl)amino]cyclohexanol C24 H31 N5 O3 S VUQJMYORHRVTLM-IYARVYRRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1J2	IC50: 3.1 - 17.9 nM (97) BINDINGDB
1J2	IC50: 6 nM BINDINGMOAD
1J2	IC50: 3 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.261 
• R-Value Work: 0.238 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 60.426	α = 90.00
b = 82.371	β = 90.00
c = 82.027	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-30 
• Released Date: 2013-12-18 
• Deposition Author(s): Kuglstatter, A., Shao, A.

Revision History 

• Version 1.0: 2013-12-18
  Type: Initial release