1VJY

Crystal Structure of a Naphthyridine Inhibitor of Human TGF-beta Type I Receptor

• PDB DOI: https://doi.org/10.2210/pdb1VJY/pdb

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


• Deposited: 2004-04-07 Released: 2004-08-31 
• Deposition Author(s): Gellibert, F., Woolven, J., Fouchet, M.-H., Mathews, N., Goodland, H., Lovegrove, V., Laroze, A., Nguyen, V.-L., Sautet, S., Wang, R., Janson, C., Smith, W., Krysa, G., Boullay, V., de Gouville, A.-C., Huet, S., Hartley, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.275 
• R-Value Work: 0.223 

Literature

Identification of 1,5-Naphthyridine Derivatives as a Novel Series of Potent and Selective TGF-beta Type I Receptor Inhibitors.

Gellibert, F., Woolven, J., Fouchet, M.-H., Mathews, N., Goodland, H., Lovegrove, V., Laroze, A., Nguyen, V.-L., Sautet, S., Wang, R., Janson, C., Smith, W., Krysa, G., Boullay, V., De Gouville, A.-C., Huet, S., Hartley, D.

(2004) J Med Chem 47: 4494-4506

• PubMed: 15317461 
• DOI: https://doi.org/10.1021/jm0400247
• Primary Citation of Related Structures:  
  1VJY


• PubMed Abstract: 
  

  Optimization of the screening hit 1 led to the identification of novel 1,5-naphthyridine aminothiazole and pyrazole derivatives, which are potent and selective inhibitors of the transforming growth factor-beta type I receptor, ALK5. Compounds 15 and 19, which inhibited ALK5 autophosphorylation with IC50 = 6 and 4 nM, respectively, showed potent activities in both binding and cellular assays and exhibited selectivity over p38 mitogen-activated protein kinase. The X-ray crystal structure of 19 in complex with human ALK5 is described, confirming the binding mode proposed from docking studies.

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Organizational Affiliation: 

Department of Medicinal Chemistry, GlaxoSmithKline, 25-27 Avenue du Québec, 91951 Les Ulis, France. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.01 kDa 
• Atom Count: 2,542 
• Modelled Residue Count: 299 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type I	A	303	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.30 (UniProt)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
460	B [auth A]	2-[5-(6-METHYLPYRIDIN-2-YL)-2,3-DIHYDRO-1H-PYRAZOL-4-YL]-1,5-NAPHTHYRIDINE C17 H15 N5 YRBHUKMLAGQYHS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
460	PDBBind:  1VJY	IC50: 23 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.275 
• R-Value Work: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.069	α = 90
b = 75.775	β = 90
c = 89.589	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNX	refinement
HKL-2000	data reduction
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-31 
Deposition Author(s): Gellibert, F., Woolven, J., Fouchet, M.-H., Mathews, N., Goodland, H., Lovegrove, V., Laroze, A., Nguyen, V.-L., Sautet, S., Wang, R., Janson, C., Smith, W., Krysa, G., Boullay, V., de Gouville, A.-C., Huet, S., Hartley, D.

Revision History  

• Version 1.0: 2004-08-31
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations