4XS2

Irak4-inhibitor co-structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery and hit-to-lead optimization of 2,6-diaminopyrimidine inhibitors of interleukin-1 receptor-associated kinase 4.

McElroy, W.T.Michael Seganish, W.Jason Herr, R.Harding, J.Yang, J.Yet, L.Komanduri, V.Prakash, K.C.Lavey, B.Tulshian, D.Greenlee, W.J.Sondey, C.Fischmann, T.O.Niu, X.

(2015) Bioorg Med Chem Lett 25: 1836-1841

  • DOI: 10.1016/j.bmcl.2015.03.043
  • Primary Citation of Related Structures:  
    4XS2

  • PubMed Abstract: 
  • Interleukin receptor-associated kinase 4 (IRAK4) is a critical element of the Toll-like/interleukin-1 receptor inflammation signaling pathway. A screening campaign identified a novel diaminopyrimidine hit that exhibits weak IRAK4 inhibitory activity ...

    Interleukin receptor-associated kinase 4 (IRAK4) is a critical element of the Toll-like/interleukin-1 receptor inflammation signaling pathway. A screening campaign identified a novel diaminopyrimidine hit that exhibits weak IRAK4 inhibitory activity and a ligand efficiency of 0.25. Hit-to-lead activities were conducted through independent SAR studies of each of the four pyrimidine substituents. Optimal activity was observed upon removal of the pyrimidine C-4 chloro substituent. The intact C-6 carboribose is required for IRAK4 inhibition. Numerous heteroaryls were tolerated at the C-5 position, with azabenzothiazoles conferring the best activities. Aminoheteroaryls were preferred at the C-2 position. These studies led to the discovery of inhibitors 35, 36, and 38 that exhibit nanomolar inhibition of IRAK4, improved ligand efficiencies, and modest kinase selectivities.


    Organizational Affiliation

    In Vitro Pharmacology, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4ABCD301Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
Find proteins for Q9NWZ3 (Homo sapiens)
Explore Q9NWZ3 
Go to UniProtKB:  Q9NWZ3
NIH Common Fund Data Resources
PHAROS  Q9NWZ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
42P
Query on 42P

Download CCD File 
A, B, C, D
(1R,2S,3R,5R)-3-({5-(1,3-benzothiazol-2-yl)-6-chloro-2-[(3-methoxypropyl)amino]pyrimidin-4-yl}amino)-5-(hydroxymethyl)cyclopentane-1,2-diol
C21 H26 Cl N5 O4 S
JCZKEQVPLPZLFI-ZPUIDXCVSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A,B,C,DL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A,B,C,DL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.97α = 90
b = 139.99β = 125.47
c = 87.62γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUSTER-TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-01-21 
  • Released Date: 2015-05-13 
  • Deposition Author(s): Fischmann, T.O.

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy