4ZTN

Irak4-inhibitor co-structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4ZTL, 4ZTM, 4ZTN

  • 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 selective pyrimidin-4-one chemotype ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4A, B, C, D301Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4S3 (Subject of Investigation/LOI)
Query on 4S3

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]5-(1,3-benzothiazol-2-yl)-2-(morpholin-4-yl)-6-[(3R)-piperidin-3-ylamino]pyrimidin-4(3H)-one
C20 H24 N6 O2 S
FWVSQXVRLKRCRX-CYBMUJFWSA-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
Binding Affinity Annotations 
IDSourceBinding Affinity
4S3 Binding MOAD:  4ZTN IC50: 19 (nM) from 1 assay(s)
BindingDB:  4ZTN IC50: min: 19, max: 4200 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.89α = 90
b = 139.18β = 125.28
c = 87.6γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
Omodel building
BUSTER-TNTphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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