4K77

JAK1 kinase (JH1 domain) in complex with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 po ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK1
A, B
302Homo sapiensMutation(s): 0 
Gene Names: JAK1 (JAK1A, JAK1B)
EC: 2.7.10.2
Find proteins for P23458 (Homo sapiens)
Go to Gene View: JAK1
Go to UniProtKB:  P23458
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1Q4
Query on 1Q4

Download SDF File 
Download CCD File 
A, B
4-(cyclohexylamino)pyrido[3,4-d]pyrimidin-8(7H)-one
C13 H16 N4 O
FCTPOQHJQPWBOI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1Q4Ki: 235 nM (100) BINDINGDB
1Q4Ki: 235 nM BINDINGMOAD
1Q4Ki: 235 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.714α = 90.00
b = 172.903β = 93.89
c = 44.547γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data reduction
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-23
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description