5KHX

Crystal structure of JAK1 in complex with PF-4950736


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.242 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6TEClick on this verticalbar to view details

This is version 1.2 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: https://doi.org/10.1107/S2053230X16016356
  • Primary Citation of Related Structures:  
    5KHW, 5KHX

  • PubMed Abstract: 

    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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1316Homo sapiensMutation(s): 0 
Gene Names: JAK1JAK1AJAK1B
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
PHAROS:  P23458
GTEx:  ENSG00000162434 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23458
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6TE
Query on 6TE

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[3-[methyl(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl]methanesulfonamide
C12 H17 N5 O2 S
QZOGHNDWZHFIJP-DTORHVGOSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
6TE BindingDB:  5KHX IC50: min: 90, max: 750 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.242 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.25α = 90
b = 88.3β = 90
c = 146.84γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6TEClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary