IRAK-4 Inhibitors (Part II)- A structure based assessment of imidazo[1,2 a]pyridine binding

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.243 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


IRAK-4 inhibitors. Part II: A structure-based assessment of imidazo[1,2-a]pyridine binding

Buckley, G.M.Ceska, T.A.Fraser, J.L.Gowers, L.Groom, C.R.Higueruelo, A.P.Jenkins, K.Mack, S.R.Morgan, T.Parry, D.M.Pitt, W.R.Rausch, O.Richard, M.D.Sabin, V.

(2008) Bioorg Med Chem Lett 18: 3291-3295

  • DOI: https://doi.org/10.1016/j.bmcl.2008.04.039
  • Primary Citation of Related Structures:  
    3CGF, 3CGO

  • PubMed Abstract: 

    A potent IRAK-4 inhibitor was identified through routine project cross screening. The binding mode was inferred using a combination of in silico docking into an IRAK-4 homology model, surrogate crystal structure analysis and chemical analogue SAR.

  • Organizational Affiliation

    UCB, Granta Park, Great Abington, Cambridge CB21 6GS, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10365Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
GTEx:  ENSG00000109339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JNO

Download Ideal Coordinates CCD File 
B [auth A]2-{4-[(4-imidazo[1,2-a]pyridin-3-ylpyrimidin-2-yl)amino]piperidin-1-yl}-N-methylacetamide
C19 H23 N7 O
Binding Affinity Annotations 
IDSourceBinding Affinity
JNO PDBBind:  3CGO IC50: 3000 (nM) from 1 assay(s)
BindingDB:  3CGO IC50: 270 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.22α = 90
b = 71.77β = 90
c = 107.72γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description