4JIA | pdb_00004jia

JAK2 kinase (JH1 domain) in complex with compound 9

• PDB DOI: https://doi.org/10.2210/pdb4JIA/pdb

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


• Deposited: 2013-03-05 Released: 2013-08-07 
• Deposition Author(s): Eigenbrot, C., Ultsch, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.202 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

2-Amino-[1,2,4]triazolo[1,5-a]pyridines as JAK2 inhibitors.

Siu, M., Pastor, R., Liu, W., Barrett, K., Berry, M., Blair, W.S., Chang, C., Chen, J.Z., Eigenbrot, C., Ghilardi, N., Gibbons, P., He, H., Hurley, C.A., Kenny, J.R., Cyrus Khojasteh, S., Le, H., Lee, L., Lyssikatos, J.P., Magnuson, S., Pulk, R., Tsui, V., Ultsch, M., Xiao, Y., Zhu, B.Y., Sampath, D.

(2013) Bioorg Med Chem Lett 23: 5014-5021

• PubMed: 23870430 
• DOI: https://doi.org/10.1016/j.bmcl.2013.06.008
• Primary Citation Related Structures: 
  4JI9, 4JIA


• PubMed Abstract: 
  

  The advancement of a series of ligand efficient 2-amino-[1,2,4]triazolo[1,5-a]pyridines, initially identified from high-throughput screening, to a JAK2 inhibitor with pharmacodynamic activity in a mouse xenograft model is disclosed.

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Organizational Affiliation: 
• Genentech, Inc, 1 DNA Way, 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: 35.85 kDa 
• Atom Count: 2,732 
• Modeled Residue Count: 300 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A	300	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1K3	B [auth A]	5-(4-methoxyphenyl)-N-[4-(4-methylpiperazin-1-yl)phenyl][1,2,4]triazolo[1,5-a]pyridin-2-amine C24 H26 N6 O DPVQBIWIVWTDRV-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.85 Å
• R-Value Free:  0.202 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.42	α = 90
b = 70.2	β = 98.95
c = 50.54	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Eigenbrot, C., Ultsch, M.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary