5UIR | pdb_00005uir

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 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 73.83 kDa 
  • Atom Count: 4,405 
  • Modeled Residue Count: 548 
  • Deposited Residue Count: 646 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8BY

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
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.277 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
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

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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
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary