Crystal structure of JAK3 in complex with peficitinib

Experimental Data Snapshot

  • Resolution: 2.67 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 

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This is version 1.2 of the entry. See complete history


Discovery and structural characterization of peficitinib (ASP015K) as a novel and potent JAK inhibitor

Hamaguchi, H.Amano, Y.Moritomo, A.Shirakami, S.Nakajima, Y.Nakai, K.Nomura, N.Ito, M.Higashi, Y.Inoue, T.

(2018) Bioorg Med Chem 26: 4971-4983

  • DOI: https://doi.org/10.1016/j.bmc.2018.08.005
  • Primary Citation of Related Structures:  
    6AAH, 6AAJ, 6AAK, 6AAM

  • PubMed Abstract: 

    Janus kinases (JAKs) are considered promising targets for the treatment of autoimmune diseases including rheumatoid arthritis (RA) due to their important role in multiple cytokine receptor signaling pathways. Recently, several JAK inhibitors have been developed for the treatment of RA. Here, we describe the identification of the novel orally bioavailable JAK inhibitor 18, peficitinib (also known as ASP015K), which showed moderate selectivity for JAK3 over JAK1, JAK2, and TYK2 in enzyme assays. Chemical modification at the C4-position of lead compound 5 led to a large increase in JAK inhibitory activity and metabolic stability in liver microsomes. Furthermore, we determined the crystal structures of JAK1, JAK2, JAK3, and TYK2 in a complex with peficitinib, and revealed that the 1H-pyrrolo[2,3-b]pyridine-5-carboxamide scaffold of peficitinib forms triple hydrogen bonds with the hinge region. Interestingly, the binding modes of peficitinib in the ATP-binding pockets differed among JAK1, JAK2, JAK3, and TYK2. WaterMap analysis of the crystal structures suggests that unfavorable water molecules are the likely reason for the difference in orientation of the 1H-pyrrolo[2,3-b]pyridine-5-carboxamide scaffold to the hinge region among JAKs.

  • Organizational Affiliation

    Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan. Electronic address: hisao.hamaguchi@astellas.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK3
A, B, C, D
287Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P52333 (Homo sapiens)
Explore P52333 
Go to UniProtKB:  P52333
PHAROS:  P52333
GTEx:  ENSG00000105639 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52333
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
A, B, C, D
Binding Affinity Annotations 
IDSourceBinding Affinity
9T6 BindingDB:  6AAK IC50: min: 0.43, max: 18 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.67 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.076α = 90
b = 114.644β = 97.65
c = 107.358γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2018-08-15 
  • Deposition Author(s): Amano, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references