3E62

Fragment based discovery of JAK-2 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3E62/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2008-08-14 Released: 2008-10-14 
• Deposition Author(s): Antonysamy, S., Fang, W., Hirst, G., Park, F., Russell, M., Smyth, L., Sprengeler, P., Stappenbeck, F., Steensma, R., Thompson, D.A., Wilson, M., Wong, M., Zhang, A., Zhang, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Fragment-based discovery of JAK-2 inhibitors.

Antonysamy, S., Hirst, G., Park, F., Sprengeler, P., Stappenbeck, F., Steensma, R., Wilson, M., Wong, M.

(2009) Bioorg Med Chem Lett 19: 279-282

• PubMed: 19019674 
• DOI: https://doi.org/10.1016/j.bmcl.2008.08.064
• Primary Citation of Related Structures:  
  3E62, 3E63, 3E64


• PubMed Abstract: 
  

  Fragment-based hit identification coupled with crystallographically enabled structure-based drug design was used to design potent inhibitors of JAK-2. After two iterations from fragment 1, we were able to increase potency by greater than 500-fold to provide sulfonamide 13, a 78-nM JAK-2 inhibitor.

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Organizational Affiliation: 

Medicinal Chemistry, SGX Pharmaceuticals, Inc, San Diego, CA 92121, USA.

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: 34.89 kDa 
• Atom Count: 2,648 
• Modelled Residue Count: 293 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A	293	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
5B1	B [auth A]	5-bromo-1H-indazol-3-amine C7 H6 Br N3 OMPYFDJVSAMSMA-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
5B1	BindingDB:  3E62	IC50: 4.09e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.302	α = 90
b = 102.297	β = 90
c = 68.386	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Antonysamy, S., Fang, W., Hirst, G., Park, F., Russell, M., Smyth, L., Sprengeler, P., Stappenbeck, F., Steensma, R., Thompson, D.A., Wilson, M., Wong, M., Zhang, A., Zhang, F.

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-01
  Changes: Structure summary
• Version 1.3: 2012-02-08
  Changes: Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary