3CGF

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

• PDB DOI: https://doi.org/10.2210/pdb3CGF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-05 Released: 2008-06-03 
• Deposition Author(s): Ceska, T.A., Platt, A., Fortunato, M., Dickson, K.M., Buckley, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.317 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 

Starting Model: experimental

Literature

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

• PubMed: 18482836 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.42 kDa 
• Atom Count: 2,831 
• Modelled Residue Count: 346 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	365	Homo sapiens	Mutation(s): 0  Gene Names: MAPK10, JNK3, JNK3A, PRKM10 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens) Explore P53779  Go to UniProtKB:  P53779
PHAROS:  P53779 GTEx:  ENSG00000109339

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JNF	B [auth A]	N-cyclohexyl-4-imidazo[1,2-a]pyridin-3-yl-N-methylpyrimidin-2-amine C18 H21 N5 HYNNWLVWJXWXFO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JNF	BindingDB:  3CGF	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.317 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.17	α = 90
b = 71.37	β = 90
c = 107.57	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Ceska, T.A., Platt, A., Fortunato, M., Dickson, K.M., Buckley, G.

Revision History  

• 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