5UIS

Crystal structure of IRAK4 in complex with compound 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/acs.jmedchem.7b00231
  • Primary Citation of Related Structures:  

  • 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 IRA ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor-associated kinase 4
A, B, C, D
323Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8C1
Query on 8C1

Download SDF File 
Download CCD File 
A, B, C, D
4-{[(3R)-piperidin-3-yl]oxy}-6-[(propan-2-yl)oxy]quinoline-7-carboxamide
C18 H23 N3 O3
WFDCRJQKOODGGI-GFCCVEGCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, B, C, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8C1IC50: 146 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.141α = 90.00
b = 141.129β = 124.72
c = 87.435γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-01-14 
  • Released Date: 2017-05-24 
  • Deposition Author(s): Han, S., Chang, J.S.

Revision History 

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