7QG1

IRAK4 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification and optimisation of a pyrimidopyridone series of IRAK4 inhibitors.

Cumming, I.A.Degorce, S.L.Aagaard, A.Braybrooke, E.L.Davies, N.L.Diene, C.R.Eatherton, A.J.Felstead, H.R.Groombridge, S.D.Lenz, E.M.Li, Y.Nai, Y.Pearson, S.Robb, G.R.Scott, J.S.Steward, O.R.Wu, C.Xue, Y.Zhang, L.Zhang, Y.

(2022) Bioorg Med Chem 63: 116729-116729

  • DOI: https://doi.org/10.1016/j.bmc.2022.116729
  • Primary Citation of Related Structures:  
    7QG1, 7QG2, 7QG3, 7QG5

  • PubMed Abstract: 

    In this article, we report the discovery of a series of pyrimidopyridones as inhibitors of IRAK4 kinase. From a previously disclosed 5-azaquinazoline series, we found that switching the pyridine ring for an N-substituted pyridone gave a novel hinge binding scaffold which retained potency against IRAK4. Importantly, introduction of the carbonyl established an internal hydrogen bond with the 4-NH, establishing a conformational lock and allowing truncation of the large basic substituent to a 1-methylcyclopyl group. Subsequent optimisation, facilitated by X-ray crystal structures, allowed identification of preferred substituents at both the pyridone core and pyrazole. Subsequent combinations of optimal groups allowed control of lipophilicity and identification of potent and selective inhibitors of IRAK4 with better in vitro permeability and lower clearance.


  • Organizational Affiliation

    Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom. Electronic address: iain.cumming@astrazeneca.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4
A, B
322Homo 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
B8I (Subject of Investigation/LOI)
Query on B8I

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
methyl 4-[4-[[6-(cyanomethyl)-2-[(1-methylpyrazol-4-yl)amino]-5-oxidanylidene-pyrido[4,3-d]pyrimidin-4-yl]amino]cyclohexyl]piperazine-1-carboxylate
C25 H32 N10 O3
HGLZLKIEOLRRSD-UAPYVXQJSA-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
B8I BindingDB:  7QG1 IC50: min: 23, max: 440 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.739α = 90
b = 109.425β = 90
c = 142.335γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary