Crystal structure of IRAK4 in complex with compound 12

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Discovery of Clinical Candidate 1-{[(2S,3S,4S)-3-Ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (PF-06650833), a Potent, Selective Inhibitor of Interleukin-1 Receptor Associated Kinase 4 (IRAK4), by Fragment-Based Drug Design.

Lee, K.L.Ambler, C.M.Anderson, D.R.Boscoe, B.P.Bree, A.G.Brodfuehrer, J.I.Chang, J.S.Choi, C.Chung, S.Curran, K.J.Day, J.E.Dehnhardt, C.M.Dower, K.Drozda, S.E.Frisbie, R.K.Gavrin, L.K.Goldberg, J.A.Han, S.Hegen, M.Hepworth, D.Hope, H.R.Kamtekar, S.Kilty, I.C.Lee, A.Lin, L.L.Lovering, F.E.Lowe, M.D.Mathias, J.P.Morgan, H.M.Murphy, E.A.Papaioannou, N.Patny, A.Pierce, B.S.Rao, V.R.Saiah, E.Samardjiev, I.J.Samas, B.M.Shen, M.W.H.Shin, J.H.Soutter, H.H.Strohbach, J.W.Symanowicz, P.T.Thomason, J.R.Trzupek, J.D.Vargas, R.Vincent, F.Yan, J.Zapf, C.W.Wright, S.W.

(2017) J Med Chem 60: 5521-5542

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00231
  • Primary Citation of Related Structures:  
    5UIQ, 5UIR, 5UIS, 5UIT, 5UIU

  • PubMed Abstract: 

    Through fragment-based drug design focused on engaging the active site of IRAK4 and leveraging three-dimensional topology in a ligand-efficient manner, a micromolar hit identified from a screen of a Pfizer fragment library was optimized to afford IRAK4 inhibitors with nanomolar potency in cellular assays. The medicinal chemistry effort featured the judicious placement of lipophilicity, informed by co-crystal structures with IRAK4 and optimization of ADME properties to deliver clinical candidate PF-06650833 (compound 40). This compound displays a 5-unit increase in lipophilic efficiency from the fragment hit, excellent kinase selectivity, and pharmacokinetic properties suitable for oral administration.

  • Organizational Affiliation

    Worldwide Medicinal Chemistry, Pfizer Inc. , 1070 Science Center Drive, San Diego, California 92121, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4
A, B, C, D
323Homo sapiensMutation(s): 0 
Gene Names: IRAK4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWZ3 (Homo sapiens)
Explore Q9NWZ3 
Go to UniProtKB:  Q9NWZ3
GTEx:  ENSG00000198001 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWZ3
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on TPO
A, B, C, D
Binding Affinity Annotations 
IDSourceBinding Affinity
8C1 BindingDB:  5UIS IC50: 146 (nM) from 1 assay(s)
Binding MOAD:  5UIS IC50: 146 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.141α = 90
b = 141.129β = 124.72
c = 87.435γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references