6O95

Structure of the IRAK4 kinase domain with compound 41


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Development of Potent and Selective Pyrazolopyrimidine IRAK4 Inhibitors.

Bryan, M.C.Drobnick, J.Gobbi, A.Kolesnikov, A.Chen, Y.Rajapaksa, N.Ndubaku, C.Feng, J.Chang, W.Francis, R.Yu, C.Choo, E.F.DeMent, K.Ran, Y.An, L.Emson, C.Huang, Z.Sujatha-Bhaskar, S.Brightbill, H.DiPasquale, A.Maher, J.Wai, J.McKenzie, B.S.Lupardus, P.J.Zarrin, A.A.Kiefer, J.R.

(2019) J.Med.Chem. 62: 6223-6240

  • DOI: 10.1021/acs.jmedchem.9b00439
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of pyrazolopyrimidine inhibitors of IRAK4 were developed from a high-throughput screen (HTS). Modification of an HTS hit led to a series of bicyclic heterocycles with improved potency and kinase selectivity but lacking sufficient solubility ...

    A series of pyrazolopyrimidine inhibitors of IRAK4 were developed from a high-throughput screen (HTS). Modification of an HTS hit led to a series of bicyclic heterocycles with improved potency and kinase selectivity but lacking sufficient solubility to progress in vivo. Structure-based drug design, informed by cocrystal structures with the protein and small-molecule crystal structures, yielded a series of dihydrobenzofurans. This semisaturated bicycle provided superior druglike properties while maintaining excellent potency and selectivity. Improved physicochemical properties allowed for progression into in vivo experiments, where lead molecules exhibited low clearance and showed target-based inhibition of IRAK4 signaling in an inflammation-mediated PK/PD mouse model.


    Organizational Affiliation

    WuXi Apptec , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone , Shanghai 200131 , P. R. China.,Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor-associated kinase 4
A, B, C, D
320Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
Find proteins for Q9NWZ3 (Homo sapiens)
Go to Gene View: IRAK4
Go to UniProtKB:  Q9NWZ3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LSV
Query on LSV

Download SDF File 
Download CCD File 
A, B, C, D
N-[(2R)-2-(hydroxymethyl)-2-methyl-6-(morpholin-4-yl)-2,3-dihydro-1-benzofuran-5-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide
C21 H23 N5 O4
JLKSBHRAVFWETB-OAQYLSRUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B, C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B, C, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.838α = 90.00
b = 140.615β = 123.71
c = 87.559γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Type: Data collection, Database references
  • Version 1.2: 2019-07-24
    Type: Data collection, Database references