4GMY

JAK2 kinase (JH1 domain) in complex with 2,6-DICHLORO-N-{2-[(CYCLOPROPYLCARBONYL)AMINO]PYRIDIN-4-YL}BENZAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.403 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Lead identification of novel and selective TYK2 inhibitors.

Liang, J.Tsui, V.Van Abbema, A.Bao, L.Barrett, K.Beresini, M.Berezhkovskiy, L.Blair, W.S.Chang, C.Driscoll, J.Eigenbrot, C.Ghilardi, N.Gibbons, P.Halladay, J.Johnson, A.Kohli, P.B.Lai, Y.Liimatta, M.Mantik, P.Menghrajani, K.Murray, J.Sambrone, A.Xiao, Y.Shia, S.Shin, Y.Smith, J.Sohn, S.Stanley, M.Ultsch, M.Zhang, B.Wu, L.C.Magnuson, S.

(2013) Eur.J.Med.Chem. 67: 175-187

  • DOI: 10.1016/j.ejmech.2013.03.070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A therapeutic rationale is proposed for the treatment of inflammatory diseases, such as psoriasis and inflammatory bowel diseases (IBD), by selective targeting of TYK2. Hit triage, following a high-throughput screen for TYK2 inhibitors, revealed pyri ...

    A therapeutic rationale is proposed for the treatment of inflammatory diseases, such as psoriasis and inflammatory bowel diseases (IBD), by selective targeting of TYK2. Hit triage, following a high-throughput screen for TYK2 inhibitors, revealed pyridine 1 as a promising starting point for lead identification. Initial expansion of 3 separate regions of the molecule led to eventual identification of cyclopropyl amide 46, a potent lead analog with good kinase selectivity, physicochemical properties, and pharmacokinetic profile. Analysis of the binding modes of the series in TYK2 and JAK2 crystal structures revealed key interactions leading to good TYK2 potency and design options for future optimization of selectivity.


    Organizational Affiliation

    Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK2
A
302Homo sapiensMutation(s): 0 
Gene Names: JAK2
EC: 2.7.10.2
Find proteins for O60674 (Homo sapiens)
Go to Gene View: JAK2
Go to UniProtKB:  O60674
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0X5
Query on 0X5

Download SDF File 
Download CCD File 
A
2,6-dichloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide
C16 H13 Cl2 N3 O2
IAFNAEGXTKTGHN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0X5Ki: 28 nM (99) BINDINGDB
0X5EC50: 1700 nM (99) BINDINGDB
0X5Ki: 28 nM BINDINGMOAD
0X5Ki: 28 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.403 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.532α = 90.00
b = 69.361β = 98.96
c = 50.468γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-16 
  • Released Date: 2013-06-19 
  • Deposition Author(s): Murray, J.M., Shia, S.

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references