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 

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

  • 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

    Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, United States.,In Vitro Pharmacology, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, United States.,Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, United States. Electronic address: william.mcelroy@merck.com.,Structural Chemistry, Merck Research Laboratories, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, United States.,Medicinal Chemistry Department, Albany Molecular Research, Inc. (AMRI), 26 Corporate Circle, Albany, NY 12203, United States.,Medicinal Chemistry Department, AMRI Singapore Research Centre, 61 Science Park Road, #05-01, The Galen, Science Park III, Singapore 117525, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor-associated kinase 4
A, B, C, D
301Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
Find proteins for Q9NWZ3 (Homo sapiens)
Go to Gene View: IRAK4
Go to UniProtKB:  Q9NWZ3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
42P
Query on 42P

Download SDF File 
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, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B, C, D
L-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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.970α = 90.00
b = 139.990β = 125.47
c = 87.620γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTERrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
BUSTER-TNTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references, Derived calculations, Refinement description, Source and taxonomy