6AAK

Crystal structure of JAK3 in complex with peficitinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1016/j.bmc.2018.08.005
  • Structures With Same Primary Citation

  • 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 bee ...

    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: inoue_eck@mii.maruho.co.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK3
A, B, C, D
287Homo sapiensMutation(s): 2 
Gene Names: JAK3
EC: 2.7.10.2
Find proteins for P52333 (Homo sapiens)
Go to UniProtKB:  P52333
NIH Common Fund Data Resources
PHAROS  P52333
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9T6
Query on 9T6

Download CCD File 
A, B, C, D
4-[[(1S,3R)-5-oxidanyl-2-adamantyl]amino]-1H-pyrrolo[2,3-b]pyridine-5-carboxamide
C18 H22 N4 O2
DREIJXJRTLTGJC-ZKVNVPQCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A,B,C,DL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-07-18 
  • Released Date: 2018-08-15 
  • Deposition Author(s): Amano, Y.

Revision History 

  • 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