5W84

CRYSTAL STRUCTURE OF IRAK-4 WITH A 4,6-DIAMINONICOTINAMIDE INHIBITOR (COMPOUND NUMBER 4)

• PDB DOI: https://doi.org/10.2210/pdb5W84/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• 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: 2.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

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 of 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].

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.

Macromolecule Content

• Total Structure Weight: 69.29 kDa 
• Atom Count: 4,324 
• Modelled Residue Count: 546 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A, B	305	Homo sapiens	Mutation(s): 0  Gene Names: IRAK4 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWZ3 (Homo sapiens) Explore Q9NWZ3  Go to UniProtKB:  Q9NWZ3
PHAROS:  Q9NWZ3 GTEx:  ENSG00000198001

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9YY	C [auth A], D [auth B]	4-(benzylamino)-6-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyridine-3-carboxamide C21 H19 N5 O2 MSYMSSQHTUWZDQ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
9YY	BindingDB:  5W84	IC50: 360 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.19	α = 90
b = 125.2	β = 90
c = 141.68	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

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: 2024-11-13
  Changes: Data collection, Database references, Structure summary