5L3A

Fragment-based discovery of 6-arylindazole JAK inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Fragment-Based Discovery of 6-Arylindazole JAK Inhibitors.

Ritzen, A.Srensen, M.D.Dack, K.N.Greve, D.R.Jerre, A.Carnerup, M.A.Rytved, K.A.Bagger-Bahnsen, J.

(2016) ACS Med Chem Lett 7: 641-646

  • DOI: https://doi.org/10.1021/acsmedchemlett.6b00087
  • Primary Citation of Related Structures:  
    5L3A

  • PubMed Abstract: 

    Janus kinase (JAK) inhibitors are emerging as novel and efficacious drugs for treating psoriasis and other inflammatory skin disorders, but their full potential is hampered by systemic side effects. To overcome this limitation, we set out to discover soft drug JAK inhibitors for topical use. A fragment screen yielded an indazole hit that was elaborated into a potent JAK inhibitor using structure-based design. Growing the fragment by installing a phenol moiety in the 6-position afforded a greatly improved potency. Fine-tuning the substituents on the phenol and sulfonamide moieties afforded a set of compounds with lead-like properties, but they were found to be phototoxic and unstable in the presence of light.


  • Organizational Affiliation

    Drug Design, In Vitro Biology, Skin PK and Early Safety, and Preformulation & Early Analytical Development, Global R&D, LEO Pharma A/S , Industriparken 55, DK-2750 Ballerup, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2295Homo sapiensMutation(s): 2 
Gene Names: JAK2
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
PHAROS:  O60674
GTEx:  ENSG00000096968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60674
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6DP
Query on 6DP

Download Ideal Coordinates CCD File 
B [auth A]~{N}-(1~{H}-indazol-4-yl)methanesulfonamide
C8 H9 N3 O2 S
CAMWAWBWBXRPRP-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6DP Binding MOAD:  5L3A Kd: 1.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.14α = 90
b = 69.7β = 98.28
c = 50.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
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: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2019-10-23
    Changes: Data collection