3DA6

Crystal Structure of human JNK3 complexed with N-(3-methyl-4-(3-(2-(methylamino)pyrimidin-4-yl)pyridin-2-yloxy)naphthalen-1-yl)-1H-benzo[d]imidazol-2-amine

• PDB DOI: https://doi.org/10.2210/pdb3DA6/pdb

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


• Deposited: 2008-05-28 Released: 2009-01-06 
• Deposition Author(s): Cee, V.J., Cheng, A.C., Romero, K., Bellon, S., Mohr, C., Whittington, D.A., Bready, J., Caenepeel, S., Coxon, A., Deak, H.L., Hodous, B.L., Kim, J.L., Lin, J., Nguyen, H., Olivieri, P.R., Patel, V.F., Wang, L., Hughes, P., Geuns-Meyer, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.320 
• R-Value Work: 0.256 
• R-Value Observed: 0.259 

Literature

Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase

Cee, V.J., Cheng, A.C., Romero, K., Bellon, S., Mohr, C., Whittington, D.A., Bak, A., Bready, J., Caenepeel, S., Coxon, A., Deak, H.L., Fretland, J., Gu, Y., Hodous, B.L., Huang, X., Kim, J.L., Lin, J., Long, A.M., Nguyen, H., Olivieri, P.R., Patel, V.F., Wang, L., Zhou, Y., Hughes, P., Geuns-Meyer, S.

(2009) Bioorg Med Chem Lett 19: 424-427

• PubMed: 19062275 
• DOI: https://doi.org/10.1016/j.bmcl.2008.11.056
• Primary Citation of Related Structures:  
  3DA6, 3EFW, 3EWH


• PubMed Abstract: 
  

  Selective small molecule inhibitors of Tie-2 kinase are important tools for the validation of Tie-2 signaling in pathological angiogenesis. Reported herein is the optimization of a nonselective scaffold into a potent and highly selective inhibitor of Tie-2 kinase.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Bldg. 1000, Cambridge, MA 02139, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.53 kDa 
• Atom Count: 2,757 
• Modelled Residue Count: 328 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	364	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
BZ9	B [auth A]	N-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)naphthalen-1-yl]-1H-benzimidazol-2-amine C28 H23 N7 O JXKDTYDBDDKIPY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BZ9	PDBBind:  3DA6	IC50: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.320 
• R-Value Work: 0.256 
• R-Value Observed: 0.259 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.483	α = 90
b = 71.283	β = 90
c = 106.957	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-06 
Deposition Author(s): Cee, V.J., Cheng, A.C., Romero, K., Bellon, S., Mohr, C., Whittington, D.A., Bready, J., Caenepeel, S., Coxon, A., Deak, H.L., Hodous, B.L., Kim, J.L., Lin, J., Nguyen, H., Olivieri, P.R., Patel, V.F., Wang, L., Hughes, P., Geuns-Meyer, S.

Revision History  

• Version 1.0: 2009-01-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations