3KCK | pdb_00003kck

A Novel Chemotype of Kinase Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3KCK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-10-21 Released: 2009-11-24 
• Deposition Author(s): Zuccola, H.J., Wang, T., Ledeboer, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.296 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

A novel chemotype of kinase inhibitors: Discovery of 3,4-ring fused 7-azaindoles and deazapurines as potent JAK2 inhibitors.

Wang, T., Ledeboer, M.W., Duffy, J.P., Pierce, A.C., Zuccola, H.J., Block, E., Shlyakter, D., Hogan, J.K., Bennani, Y.L.

(2010) Bioorg Med Chem Lett 20: 153-156

• PubMed: 19945871 
• DOI: https://doi.org/10.1016/j.bmcl.2009.11.021
• Primary Citation Related Structures: 
  3KCK


• PubMed Abstract: 
  

  Pictet-Spengler condensation of aldehydes or alpha-keto-esters with 4-(2-anilinophenyl)-7-azaindole (11) or deazapurine (12) gave high yields of the 3,4-fused cyclic compounds. SAR studies, by varying the substituted benzaldehyde components, lead to the discovery of a series of potent JAK2 kinase inhibitors.

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Organizational Affiliation: 
• Vertex Pharmaceuticals Inc., 130 Waverly St., Cambridge, MA 02139-4242, 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: 37.13 kDa 
• Atom Count: 2,506 
• Modeled Residue Count: 287 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A	313	Homo sapiens	Mutation(s): 0  Gene Names: JAK2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens) Explore O60674  Go to UniProtKB:  O60674
PHAROS:  O60674 GTEx:  ENSG00000096968

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3KC	B [auth A]	3-chloro-4-(4H-3,4,7-triazadibenzo[cd,f]azulen-6-yl)phenol C20 H12 Cl N3 O JBHMPWHPXOOFNL-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.296 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.156	α = 90
b = 100.803	β = 90
c = 67.621	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
d*TREK	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Zuccola, H.J., Wang, T., Ledeboer, M.W.

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary