4K6Z

The Jak1 kinase domain in complex with compound 37


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design and evaluation of novel 8-oxo-pyridopyrimidine Jak1/2 inhibitors.

Labadie, S.Barrett, K.Blair, W.S.Chang, C.Deshmukh, G.Eigenbrot, C.Gibbons, P.Johnson, A.Kenny, J.R.Kohli, P.B.Liimatta, M.Lupardus, P.J.Shia, S.Steffek, M.Ubhayakar, S.Abbema, A.V.Zak, M.

(2013) Bioorg Med Chem Lett 23: 5923-5930

  • DOI: 10.1016/j.bmcl.2013.08.082
  • Primary Citation of Related Structures:  
    4K6Z, 4K77

  • PubMed Abstract: 
  • A highly ligand efficient, novel 8-oxo-pyridopyrimidine containing inhibitor of Jak1 and Jak2 isoforms with a pyridone moiety as the hinge-binding motif was discovered. Structure-based design strategies were applied to significantly improve enzyme potency and the polarity of the molecule was adjusted to gain cellular activity ...

    A highly ligand efficient, novel 8-oxo-pyridopyrimidine containing inhibitor of Jak1 and Jak2 isoforms with a pyridone moiety as the hinge-binding motif was discovered. Structure-based design strategies were applied to significantly improve enzyme potency and the polarity of the molecule was adjusted to gain cellular activity. The crystal structures of two representative inhibitors bound to Jak1 were obtained to enable SAR exploration.


    Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: sharadal@gene.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1 A302Homo sapiensMutation(s): 0 
Gene Names: JAK1JAK1AJAK1B
EC: 2.7.10.2
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
NIH Common Fund Data Resources
PHAROS:  P23458
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1Q3
Query on 1Q3

Download Ideal Coordinates CCD File 
A
(1R,2S)-2-{[8-oxo-2-(1H-pyrazol-4-yl)-5,8-dihydropyrido[3,4-d]pyrimidin-4-yl]amino}cyclopentanecarbonitrile
C16 H15 N7 O
GGNYHYINELGWQU-CABZTGNLSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1Q3Ki :  2   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.574α = 90
b = 42.701β = 90
c = 44.301γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references