3LPB

Crystal structure of Jak2 complexed with a potent 2,8-diaryl-quinoxaline inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LPB/pdb

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


• Deposited: 2010-02-05 Released: 2010-04-28 
• Deposition Author(s): Tavares, G.A., Pissot-Soldermann, C., Gerspacher, M., Furet, P., Kroemer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Discovery and SAR of potent, orally available 2,8-diaryl-quinoxalines as a new class of JAK2 inhibitors

Pissot-Soldermann, C., Gerspacher, M., Furet, P., Gaul, C., Holzer, P., McCarthy, C., Radimerski, T., Regnier, C.H., Baffert, F., Drueckes, P., Tavares, G.A., Vangrevelinghe, E., Blasco, F., Ottaviani, G., Ossola, F., Scesa, J., Reetz, J.

(2010) Bioorg Med Chem Lett 20: 2609-2613

• PubMed: 20231096 
• DOI: https://doi.org/10.1016/j.bmcl.2010.02.056
• Primary Citation of Related Structures:  
  3LPB


• PubMed Abstract: 
  

  We have designed and synthesized a novel series of 2,8-diaryl-quinoxalines as Janus kinase 2 inhibitors. Many of the inhibitors show low nanomolar activity against JAK2 and potently suppress proliferation of SET-2 cells in vitro. In addition, compounds from this series have favorable rat pharmacokinetic properties suitable for in vivo efficacy evaluation.

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Organizational Affiliation: 

Novartis Institutes for Biomedical Research, Novartis Pharma AG, WKL-136.4.96, CH-4002 Basel, Switzerland. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.38 kDa 
• Atom Count: 4,944 
• Modelled Residue Count: 566 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A, B	295	Homo sapiens	Mutation(s): 0  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
NVB	C [auth A], D [auth B]	N-methyl-4-[3-(3,4,5-trimethoxyphenyl)quinoxalin-5-yl]benzenesulfonamide C24 H23 N3 O5 S LYSCAOWDVVWGQK-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
NVB	BindingDB:  3LPB	IC50: 42 (nM) from 1 assay(s)
	PDBBind:  3LPB	IC50: 42 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.39	α = 90
b = 112.39	β = 90
c = 70.651	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Tavares, G.A., Pissot-Soldermann, C., Gerspacher, M., Furet, P., Kroemer, M.

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary