5UIU

Crystal structure of IRAK4 in complex with compound 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4
A, B
323Homo 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
GTEx:  ENSG00000198001 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWZ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8CG
Query on 8CG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1-{[(2S,3S,4S)-3-ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide
C18 H20 F N3 O4
JKDGKIBAOAFRPJ-ZBINZKHDSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
8CG BindingDB:  5UIU IC50: min: 0.1, max: 2 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.94α = 90
b = 118.46β = 90
c = 138.84γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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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