5KX7 | pdb_00005kx7

Irak4-inhibitor co-structure

• PDB DOI: https://doi.org/10.2210/pdb5KX7/pdb

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


• Deposited: 2016-07-20 Released: 2016-08-17 
• Deposition Author(s): Fischmann, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.250 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Efforts towards the optimization of a bi-aryl class of potent IRAK4 inhibitors.

Hanisak, J., Seganish, W.M., McElroy, W.T., Tang, H., Zhang, R., Tsui, H.C., Fischmann, T., Tulshian, D., Tata, J., Sondey, C., Devito, K., Fossetta, J., Garlisi, C.G., Lundell, D., Niu, X.

(2016) Bioorg Med Chem Lett 26: 4250-4255

• PubMed: 27476420 
• DOI: https://doi.org/10.1016/j.bmcl.2016.07.048
• Primary Citation Related Structures: 
  5KX7, 5KX8


• PubMed Abstract: 
  

  IRAK4 has been identified as potential therapeutic target for inflammatory and autoimmune diseases. Herein we report the identification and initial SAR studies of a new class of pyrazole containing IRAK4 inhibitors designed to expand chemical diversity and improve off target activity of a previously identified series. These compounds maintain potent IRAK4 activity and desirable ligand efficiency. Rat clearance and a variety of off target activities were also examined, resulting in encouraging data with tractable SAR.

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Organizational Affiliation: 
• Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, Unites States. Electronic address: [e-mail].
Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, Unites States.
In Vitro Pharmacology, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, United States.
Respiratory and Immunology, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, United States.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.24 kDa 
• Atom Count: 4,159 
• Modeled Residue Count: 529 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A, B	301	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
6YD	C [auth B]	~{N}-(3-aminocarbonyl-1-methyl-pyrazol-4-yl)-6-(1-methylpyrazol-4-yl)pyridine-2-carboxamide C15 H15 N7 O2 XTVOMCVEGADMQN-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.250 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.8	α = 90
b = 114.28	β = 90
c = 139.44	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Fischmann, T.O.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary