6O94

Structure of the IRAK4 kinase domain with compound 17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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:  
    6O9D, 6O95, 6O94, 6O8U

  • 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

    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, D320Homo 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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LRS
Query on LRS

Download CCD File 
A, B, C, D
N-{5-[4-(hydroxymethyl)piperidin-1-yl]-1-methyl-2-(morpholin-4-yl)-1H-benzimidazol-6-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide
C25 H30 N8 O3
LVDMRCKBQDTUEU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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 %)
LRSKi:  7.400000095367432   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.545α = 90
b = 140.111β = 123.36
c = 87.822γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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