6RFJ | pdb_00006rfj

IRAK4 IN COMPLEX WITH inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.254 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6RFJ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of a Series of 5-Azaquinazolines as Orally Efficacious IRAK4 Inhibitors Targeting MyD88L265PMutant Diffuse Large B Cell Lymphoma.

Degorce, S.L.Anjum, R.Bloecher, A.Carbajo, R.J.Dillman, K.S.Drew, L.Halsall, C.T.Lenz, E.M.Lindsay, N.A.Mayo, M.F.Pink, J.H.Robb, G.R.Rosen, A.Scott, J.S.Xue, Y.

(2019) J Med Chem 62: 9918-9930

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01346
  • Primary Citation Related Structures: 
    6RFI, 6RFJ

  • PubMed Abstract: 

    In this article, we report the discovery of a series of 5-azaquinazolines as selective IRAK4 inhibitors. From modestly potent quinazoline 4 , we introduced a 5-aza substitution to mask the 4-NH hydrogen bond donor (HBD). This allowed us to substitute the core with a 2-aminopyrazole, which showed large gains in cellular potency despite the additional formal HBD. Further optimization led to 6-cyanomethyl-5-azaquinazoline 13 , a selective IRAK4 inhibitor, which proved efficacious in combination with ibrutinib, while showing very little activity as a single agent up to 100 mg/kg. This contrasted to previously reported IRAK4 inhibitors that exhibited efficacy in the same model as single agents and was attributed to the enhanced specificity of 13 toward IRAK4.


  • Organizational Affiliation
    • Medicinal Chemistry, Oncology R&D , AstraZeneca , Cambridge Science Park , Unit 310 Darwin Building, Cambridge CB4 0WG , U.K.

Macromolecule Content 

  • Total Structure Weight: 74.16 kDa 
  • Atom Count: 4,450 
  • Modeled Residue Count: 547 
  • Deposited Residue Count: 644 
  • 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
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K1E

Query on K1E



Download:Ideal Coordinates CCD File
C [auth A],
E [auth B]
methyl 4-[4-[[6-(cyanomethyl)-2-[(1-methylpyrazol-4-yl)amino]pyrido[3,2-d]pyrimidin-4-yl]amino]cyclohexyl]piperazine-1-carboxylate
C25 H32 N10 O2
RPGMSHCJIWHISY-IRJFHVNHSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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
K1E BindingDB:  6RFJ IC50: min: 3, max: 170 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.254 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.607α = 90
b = 118.925β = 90
c = 140.507γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary