5KHX

Crystal structure of JAK1 in complex with PF-4950736


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of a high-throughput crystal structure-determination platform for JAK1 using a novel metal-chelator soaking system.

Caspers, N.L.Han, S.Rajamohan, F.Hoth, L.R.Geoghegan, K.F.Subashi, T.A.Vazquez, M.L.Kaila, N.Cronin, C.N.Johnson, E.Kurumbail, R.G.

(2016) Acta Crystallogr F Struct Biol Commun 72: 840-845

  • DOI: 10.1107/S2053230X16016356
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystals of phosphorylated JAK1 kinase domain were initially generated in complex with nucleotide (ADP) and magnesium. The tightly bound Mg <sup>2+ </sup>-ADP at the ATP-binding site proved recalcitrant to ligand displacement. Addition of a molar exc ...

    Crystals of phosphorylated JAK1 kinase domain were initially generated in complex with nucleotide (ADP) and magnesium. The tightly bound Mg 2+ -ADP at the ATP-binding site proved recalcitrant to ligand displacement. Addition of a molar excess of EDTA helped to dislodge the divalent metal ion, promoting the release of ADP and allowing facile exchange with ATP-competitive small-molecule ligands. Many kinases require the presence of a stabilizing ligand in the ATP site for crystallization. This procedure could be useful for developing co-crystallization systems with an exchangeable ligand to enable structure-based drug design of other protein kinases.


    Organizational Affiliation

    Structural Biology, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA.,Inflammation Medicinal Chemistry, Pfizer Inc., 610 Main Street, Cambridge, MA 02139, USA.,Oncology Structural Biology, Pfizer Inc., 10770 Science Center Drive, San Diego, CA 92121, USA.,Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK1
A
316Homo 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
6TE
Query on 6TE

Download SDF File 
Download CCD File 
A
~{N}-[3-[methyl(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl]methanesulfonamide
C12 H17 N5 O2 S
QZOGHNDWZHFIJP-DTORHVGOSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 46.250α = 90.00
b = 88.300β = 90.00
c = 146.840γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
BUSTERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-16 
  • Released Date: 2016-11-09 
  • Deposition Author(s): Han, S., Caspers, N.L.

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references, Derived calculations