6O8U

Crystal structure of IRAK4 in complex with compound 23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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Ligand Structure Quality Assessment 


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:  
    6O8U, 6O94, 6O95, 6O9D

  • 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 to progress in vivo ...

    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

    Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4A, B, C, D305Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
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
Binding Affinity Annotations 
IDSourceBinding Affinity
LS7 Binding MOAD:  6O8U Ki: 5.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.119α = 90
b = 140.511β = 123.97
c = 87.518γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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