4ZTM

Irak4-inhibitor co-structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery and Structure Enabled Synthesis of 2,6-Diaminopyrimidin-4-one IRAK4 Inhibitors.

Seganish, W.M.Fischmann, T.O.Sherborne, B.Matasi, J.Lavey, B.McElroy, W.T.Tulshian, D.Tata, J.Sondey, C.Garlisi, C.G.Devito, K.Fossetta, J.Lundell, D.Niu, X.

(2015) Acs Med.Chem.Lett. 6: 942-947

  • DOI: 10.1021/acsmedchemlett.5b00279
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the identification and synthesis of a series of aminopyrimidin-4-one IRAK4 inhibitors. Through high throughput screening, an aminopyrimidine hit was identified and modified via structure enabled design to generate a new, potent, and kinase ...

    We report the identification and synthesis of a series of aminopyrimidin-4-one IRAK4 inhibitors. Through high throughput screening, an aminopyrimidine hit was identified and modified via structure enabled design to generate a new, potent, and kinase selective pyrimidin-4-one chemotype. This chemotype is exemplified by compound 16, which has potent IRAK4 inhibition activity (IC50 = 27 nM) and excellent kinase selectivity (>100-fold against 99% of 111 tested kinases), and compound 31, which displays potent IRAK4 activity (IC50 = 93 nM) and good rat bioavailability (F = 42%).


    Organizational Affiliation

    Discovery Chemistry, Structural Sciences, Computational Chemistry, In Vitro Pharmacology, and Respiratory and Immunology, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.




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
4S2
Query on 4S2

Download SDF File 
Download CCD File 
A, B, C, D
5-(1,3-benzothiazol-2-yl)-2-(cyclopropylamino)-6-{[(1R,2S,3R,4R)-2,3-dihydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyrimidin-4(3H)-one
C20 H23 N5 O4 S
FXWUDZUPMZEZQL-NRXFTUCASA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4S2IC50: 25 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.930α = 90.00
b = 139.250β = 124.26
c = 87.770γ = 90.00
Software Package:
Software NamePurpose
Omodel building
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERrefinement
BUSTER-TNTphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-05-14 
  • Released Date: 2015-09-02 
  • Deposition Author(s): Fischmann, T.O.

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release