4D2R | pdb_00004d2r

Human IGF in complex with a Dyrk1B inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4D2R/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-05-12 Released: 2015-04-22 
• Deposition Author(s): Debreczeni, J.E., Kettle, J.G., Ballard, P., Bardelle, C., Butterworth, S., Colclough, N., Critchlow, S.E., Fairley, G., Fillery, S., Graham, M.A., Goodwin, L., Guichard, S., Hudson, K., Mahmood, A., Vincent, J., Ward, R.A., Whittaker, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Discovery and Optimization of a Novel Series of Dyrk1B Kinase Inhibitors to Explore a Mek Resistance Hypothesis.

Kettle, J.G., Ballard, P., Bardelle, C., Cockerill, M., Colclough, N., Critchlow, S.E., Debreczeni, J.E., Fairley, G., Fillery, S., Graham, M.A., Goodwin, L., Guichard, S., Hudson, K., Ward, R.A., Whittaker, D.

(2015) J Med Chem 58: 2834

• PubMed: 25738750 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00098
• Primary Citation of Related Structures:  
  4D2R, 4D2S


• PubMed Abstract: 
  

  Potent and selective inhibitors of Dyrk1B kinase were developed to explore the hypothesis, based on siRNA studies, that Dyrk1B may be a resistance mechanism in cells undergoing a stress response.

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Organizational Affiliation: 

Oncology iMed, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, United Kingdom.

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: 35.05 kDa 
• Atom Count: 2,602 
• Modelled Residue Count: 300 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INSULIN-LIKE GROWTH FACTOR 1 RECEPTOR	A	302	Homo sapiens	Mutation(s): 0  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08069 (Homo sapiens) Explore P08069  Go to UniProtKB:  P08069
PHAROS:  P08069 GTEx:  ENSG00000140443

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DYK	C [auth A]	N-{2-methoxy-4-[(1-methylpiperidin-4-yl)oxy]phenyl}-4-(1H-pyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine C24 H26 N6 O2 FTZQWKAIKYEWPM-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
DYK	BindingDB:  4D2R	IC50: 3300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.154	α = 90
b = 66.486	β = 90
c = 121.593	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Debreczeni, J.E., Kettle, J.G., Ballard, P., Bardelle, C., Butterworth, S., Colclough, N., Critchlow, S.E., Fairley, G., Fillery, S., Graham, M.A., Goodwin, L., Guichard, S., Hudson, K., Mahmood, A., Vincent, J., Ward, R.A., Whittaker, D.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection
• Version 1.2: 2019-10-23
  Changes: Data collection, Experimental preparation, Other, Structure summary
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations