2WOT

ALK5 IN COMPLEX WITH 4-((5,6-dimethyl-2-(2-pyridyl)-3-pyridyl)oxy)-N-(3,4,5-trimethoxyphenyl)pyridin-2-amine

• PDB DOI: https://doi.org/10.2210/pdb2WOT/pdb

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


• Deposited: 2009-07-28 Released: 2009-09-22 
• Deposition Author(s): Norman, R.A., Debreczeni, J.E., Goldberg, F.W., Ward, R.A., Finlay, R., Powell, S.J., Roberts, N.J., Dishington, A.P., Gingell, H.J., Wickson, K.F., Roberts, A.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.221 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Rapid Generation of a High Quality Lead for Transforming Growth Factor-Beta (Tgf-Beta) Type I Receptor (Alk5).

Goldberg, F.W., Ward, R.A., Powell, S.J., Debreczeni, J.E., Norman, R.A., Roberts, N.J., Dishington, A.P., Gingell, H.J., Wickson, K.F., Roberts, A.L.

(2009) J Med Chem 52: 7901

• PubMed: 19736928 
• DOI: https://doi.org/10.1021/jm900807w
• Primary Citation of Related Structures:  
  2WOT, 2WOU


• PubMed Abstract: 
  

  A novel class of 4-pyridinoxy-2-anilinopyridine-based TGF-beta type I receptor (also known as activin-like kinase 5 or ALK5) inhibitors is reported. The binding mode of this scaffold was successfully predicted by analyzing possible docked binding modes of literature inhibitors and novel synthetic ideas. Compounds such as 19 are potent ALK5 inhibitors with good physicochemical and pharmacokinetic properties and thus represent high quality leads for further optimization.

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Organizational Affiliation: 

AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, 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: 35.46 kDa 
• Atom Count: 2,768 
• Modelled Residue Count: 303 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-BETA RECEPTOR TYPE-1	A	306	Homo sapiens	Mutation(s): 0  EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P36897 (Homo sapiens) Explore P36897  Go to UniProtKB:  P36897
PHAROS:  P36897 GTEx:  ENSG00000106799

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZZG	B [auth A]	4-[(5,6-DIMETHYL-2,2'-BIPYRIDIN-3-YL)OXY]-N-(3,4,5-TRIMETHOXYPHENYL)PYRIDIN-2-AMINE C26 H26 N4 O4 RNLQQRFAMDEKKT-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZZG	BindingDB:  2WOT	IC50: 44 (nM) from 1 assay(s)
		EC50: 55 (nM) from 1 assay(s)
	PDBBind:  2WOT	IC50: 44 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.221 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.933	α = 90
b = 78.218	β = 90
c = 89.074	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Norman, R.A., Debreczeni, J.E., Goldberg, F.W., Ward, R.A., Finlay, R., Powell, S.J., Roberts, N.J., Dishington, A.P., Gingell, H.J., Wickson, K.F., Roberts, A.L.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-11-23
  Changes: Database references, Structure summary
• Version 1.3: 2014-11-19
  Changes: Data collection
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 1.5: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.6: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other