5UIR

Crystal structure of IRAK4 in complex with compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4A, B323Homo 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
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8BY (Subject of Investigation/LOI)
Query on 8BY

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]5-(4-cyanophenyl)-3-[(propan-2-yl)oxy]naphthalene-2-carboxamide
C21 H18 N2 O2
IDCYKLUUMJIGRR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, BL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, BL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
8BY BindingDB:  5UIR IC50: 72 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.695α = 90
b = 110.859β = 90
c = 140.491γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

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