5L3A | pdb_00005l3a

Fragment-based discovery of 6-arylindazole JAK inhibitors

• PDB DOI: https://doi.org/10.2210/pdb5L3A/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-04-06 Released: 2016-04-27 
• Deposition Author(s): Soerensen, M.D., Dack, K.N., Greve, D.R., Ritzen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.277 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.233 (Depositor) 
• R-Value Observed: 
  0.235 (Depositor) 

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

• PubMed: 27326341 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00087
• Primary Citation 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.74 kDa 
• Atom Count: 2,454 
• Modeled Residue Count: 290 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A	295	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6DP	B [auth A]	~{N}-(1~{H}-indazol-4-yl)methanesulfonamide C8 H9 N3 O2 S CAMWAWBWBXRPRP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6DP	BindingDB:  5L3A	Kd: 1.26e+4 (nM) from 1 assay(s)
		IC50: 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 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.233 (Depositor) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.14	α = 90
b = 69.7	β = 98.28
c = 50.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Soerensen, M.D., Dack, K.N., Greve, D.R., Ritzen, A.

Revision History  

• 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
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references