4Y73

Crystal structure of IRAK4 kinase domain with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of 5-Amino-N-(1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamide Inhibitors of IRAK4.

Lim, J.Altman, M.D.Baker, J.Brubaker, J.D.Chen, H.Chen, Y.Fischmann, T.Gibeau, C.Kleinschek, M.A.Leccese, E.Lesburg, C.Maclean, J.K.Moy, L.Y.Mulrooney, E.F.Presland, J.Rakhilina, L.Smith, G.F.Steinhuebel, D.Yang, R.

(2015) ACS Med Chem Lett 6: 683-688

  • DOI: 10.1021/acsmedchemlett.5b00107
  • Primary Citation of Related Structures:  
    4Y73

  • PubMed Abstract: 
  • Interleukin-1 receptor associated kinase 4 (IRAK4) is an essential signal transducer downstream of the IL-1R and TLR superfamily, and selective inhibition of the kinase activity of the protein represents an attractive target for the treatment of infl ...

    Interleukin-1 receptor associated kinase 4 (IRAK4) is an essential signal transducer downstream of the IL-1R and TLR superfamily, and selective inhibition of the kinase activity of the protein represents an attractive target for the treatment of inflammatory diseases. A series of 5-amino-N-(1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamides was developed via sequential modifications to the 5-position of the pyrazolopyrimidine ring and the 3-position of the pyrazole ring. Replacement of substituents responsible for poor permeability and improvement of physical properties guided by cLogD led to the identification of IRAK4 inhibitors with excellent potency, kinase selectivity, and pharmacokinetic properties suitable for oral dosing.


    Organizational Affiliation

    Departments of Chemistry, Immunology, Chemistry Modeling and Informatics, Drug Metabolism and Pharmacokinetics, In Vitro Pharmacology, In Vivo Pharmacology, and Structural Chemistry, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4ABCD302Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
Find proteins for Q9NWZ3 (Homo sapiens)
Explore Q9NWZ3 
Go to UniProtKB:  Q9NWZ3
NIH Common Fund Data Resources
PHAROS  Q9NWZ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XPY
Query on XPY

Download CCD File 
A, B, C, D
5-{[(1R,2S)-2-aminocyclohexyl]amino}-N-[1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide
C18 H21 F3 N8 O
LAXFSYWLDNVHAQ-NWDGAFQWSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A,B,C,DL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A,B,C,DL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XPYIC50:  0.30000001192092896   nM  Binding MOAD
XPYIC50:  0.5   nM  BindingDB
XPYIC50:  9   nM  BindingDB
XPYIC50:  0.30000001192092896   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.86α = 90
b = 138.75β = 124.59
c = 88.02γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-02-13 
  • Released Date: 2015-05-20 
  • Deposition Author(s): Lesburg, C.A.

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references