6HZU | pdb_00006hzu

HUMAN JAK1 IN COMPLEX WITH LASW1393


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.265 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6HZU

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification of 2-Imidazopyridine and 2-Aminopyridone Purinones as Potent Pan-Janus Kinase (JAK) Inhibitors for the Inhaled Treatment of Respiratory Diseases.

Bach, J.Eastwood, P.Gonzalez, J.Gomez, E.Alonso, J.A.Fonquerna, S.Lozoya, E.Orellana, A.Maldonado, M.Calaf, E.Alberti, J.Perez, J.Andres, A.Prats, N.Carreno, C.Calama, E.De Alba, J.Calbet, M.Miralpeix, M.Ramis, I.

(2019) J Med Chem 62: 9045-9060

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00533
  • Primary Citation Related Structures: 
    6HZU, 6HZV

  • PubMed Abstract: 

    Janus kinases (JAKs) have a key role in regulating the expression and function of relevant inflammatory cytokines involved in asthma and chronic obstructive pulmonary disease. Herein are described the design, synthesis, and pharmacological evaluation of a series of novel purinone JAK inhibitors with profiles suitable for inhaled administration. Replacement of the imidazopyridine hinge binding motif present in the initial compounds of this series with a pyridone ring resulted in the mitigation of cell cytotoxicity. Further systematic structure-activity relationship (SAR) efforts driven by structural biology studies led to the discovery of pyridone 34 , a potent pan-JAK inhibitor with good selectivity, long lung retention time, low oral bioavailability, and proven efficacy in the lipopolysaccharide-induced rat model of airway inflammation by the inhaled route.

Macromolecule Content 

  • Total Structure Weight: 70.22 kDa 
  • Atom Count: 5,103 
  • Modeled Residue Count: 579 
  • Deposited Residue Count: 604 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1
A, B
302Homo sapiensMutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GYQ

Query on GYQ



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2-[4-[8-oxidanylidene-2-[(~{E})-(2-oxidanylidenepyridin-3-ylidene)amino]-7~{H}-purin-9-yl]cyclohexyl]ethanenitrile
C18 H17 N7 O2
JCBSNZZSUFHWSE-UGHOIBRWSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.265 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.794α = 90
b = 173.763β = 94.24
c = 44.864γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-09
    Changes: Advisory, Data collection, Database references, Structure summary