3TTI

Crystal Structure of JNK3 complexed with CC-930, an orally active anti-fibrotic JNK inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb3TTI/pdb

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


• Deposited: 2011-09-14 Released: 2012-02-01 
• Deposition Author(s): Plantevin-Krenitsky, V., Nadolny, L., Delgado, M., Ayala, L., Clareen, S., Hilgraf, R., Albers, R., Hegde, S., D'Sidocky, N., Sapienza, J., Wright, J., McCarrick, M., Bahmanyar, S., Chamberlain, P., Delker, S.L., Muir, J., Giegel, D., Xu, L., Celeridad, M., Lachowitzer, J., Bennett, B., Moghaddam, M., Khatsenko, O., Katz, J., Fan, R., Bai, A., Tang, Y., Shirley, M.A., Benish, B., Bodine, T., Blease, K., Raymon, H., Cathers, B.E., Satoh, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.335 
• R-Value Work: 0.242 
• R-Value Observed: 0.246 

Literature

Discovery of CC-930, an orally active anti-fibrotic JNK inhibitor.

Plantevin Krenitsky, V., Nadolny, L., Delgado, M., Ayala, L., Clareen, S.S., Hilgraf, R., Albers, R., Hegde, S., D'Sidocky, N., Sapienza, J., Wright, J., McCarrick, M., Bahmanyar, S., Chamberlain, P., Delker, S.L., Muir, J., Giegel, D., Xu, L., Celeridad, M., Lachowitzer, J., Bennett, B., Moghaddam, M., Khatsenko, O., Katz, J., Fan, R., Bai, A., Tang, Y., Shirley, M.A., Benish, B., Bodine, T., Blease, K., Raymon, H., Cathers, B.E., Satoh, Y.

(2012) Bioorg Med Chem Lett 22: 1433-1438

• PubMed: 22244937 
• DOI: https://doi.org/10.1016/j.bmcl.2011.12.027
• Primary Citation of Related Structures:  
  3TTI


• PubMed Abstract: 
  

  In this Letter we describe the discovery of potent, selective, and orally active aminopurine JNK inhibitors. Improving the physico-chemical properties as well as increasing the potency and selectivity of a subseries with rat plasma exposure, led to the identification of four structurally diverse inhibitors. Differentiation based on PK profiles in multiple species as well as activity in a chronic efficacy model led to the identification of 1 (CC-930) as a development candidate, which is currently in Phase II clinical trial for IPF.

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Organizational Affiliation: 

Celgene Corporation, 4550 Towne Centre Court, San Diego, CA 92121, USA. [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: 53.19 kDa 
• Atom Count: 3,032 
• Modelled Residue Count: 341 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	464	Homo sapiens	Mutation(s): 0  Gene Names: JNK3, JNK3A, MAPK10, PRKM10, SAPK1B 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KBI	B [auth A]	trans-4-({9-[(3S)-tetrahydrofuran-3-yl]-8-[(2,4,6-trifluorophenyl)amino]-9H-purin-2-yl}amino)cyclohexanol C21 H23 F3 N6 O2 IBGLGMOPHJQDJB-IHRRRGAJSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KBI	BindingDB:  3TTI	Ki: 44 (nM) from 1 assay(s)
		IC50: min: 6, max: 61 (nM) from 2 assay(s)
	PDBBind:  3TTI	IC50: 6 (nM) from 1 assay(s)
	Binding MOAD:  3TTI	IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.335 
• R-Value Work: 0.242 
• R-Value Observed: 0.246 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.189	α = 90
b = 71.202	β = 90
c = 106.813	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Plantevin-Krenitsky, V., Nadolny, L., Delgado, M., Ayala, L., Clareen, S., Hilgraf, R., Albers, R., Hegde, S., D'Sidocky, N., Sapienza, J., Wright, J., McCarrick, M., Bahmanyar, S., Chamberlain, P., Delker, S.L., Muir, J., Giegel, D., Xu, L., Celeridad, M., Lachowitzer, J., Bennett, B., Moghaddam, M., Khatsenko, O., Katz, J., Fan, R., Bai, A., Tang, Y., Shirley, M.A., Benish, B., Bodine, T., Blease, K., Raymon, H., Cathers, B.E., Satoh, Y.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2012-02-08
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description