5W86 | pdb_00005w86

CRYSTAL STRUCTURE OF JAK3 KINASE DOMAIN WITH A 4,6-DIAMINONICOTINAMIDE INHIBITOR (COMPOUND NUMBER 7)

• PDB DOI: https://doi.org/10.2210/pdb5W86/pdb

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


• Deposited: 2017-06-21 Released: 2017-10-11 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.264 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Discovery and structure-based design of 4,6-diaminonicotinamides as potent and selective IRAK4 inhibitors.

Bhide, R.S., Keon, A., Weigelt, C., Sack, J.S., Schmidt, R.J., Lin, S., Xiao, H.Y., Spergel, S.H., Kempson, J., Pitts, W.J., Carman, J., Poss, M.A.

(2017) Bioorg Med Chem Lett 27: 4908-4913

• PubMed: 28947151 
• DOI: https://doi.org/10.1016/j.bmcl.2017.09.029
• Primary Citation Related Structures: 
  5W84, 5W85, 5W86


• PubMed Abstract: 
  

  The identification of small molecule inhibitors of IRAK4 for the treatment of autoimmune diseases has been an area of intense research. We discovered novel 4,6-diaminonicotinamides which potently inhibit IRAK4. Optimization efforts were aided by X-ray crystal structures of inhibitors bound to IRAK4. Structure activity relationship (SAR) studies led to the identification of compound 29 which exhibited sub-micromolar potency in a LTA stimulated cellular assay.

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Organizational Affiliation: 
• Discovery Chemistry, Research & Development, Bristol-Myers Squibb Company, Route 206 & Province Line Road, Princeton, NJ 08543, United States. Electronic address: [e-mail].
Discovery Chemistry, Research & Development, Bristol-Myers Squibb Company, Route 206 & Province Line Road, Princeton, NJ 08543, United States.
Molecular Structure and Design, Research & Development, Bristol-Myers Squibb Company, Route 206 & Province Line Road, Princeton, NJ 08543, United States.
Immunoscience Biology, Research & Development, Bristol-Myers Squibb Company, Route 206 & Province Line Road, Princeton, NJ 08543, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 133.27 kDa 
• Atom Count: 8,915 
• Modeled Residue Count: 1,089 
• Deposited Residue Count: 1,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK3	A, B, C, D	287	Homo sapiens	Mutation(s): 2  Gene Names: JAK3 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P52333 (Homo sapiens) Explore P52333  Go to UniProtKB:  P52333
PHAROS:  P52333 GTEx:  ENSG00000105639

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9YV	E [auth A], F [auth B], G [auth C], H [auth D]	4-(benzylamino)-6-({4-[(1-methylpiperidin-4-yl)carbamoyl]phenyl}amino)pyridine-3-carboxamide C26 H30 N6 O2 NYSLPKXXILEKDL-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B, C, D	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
9YV	BindingDB:  5W86	IC50: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.264 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.983	α = 90
b = 112.297	β = 90.06
c = 97.119	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Sack, J.S.

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary