5USQ | pdb_00005usq

ALK-5 kinase inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb5USQ/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2017-02-13 Released: 2017-04-12 
• Deposition Author(s): Dougan, D.R., Lawson, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.231 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Design, synthesis and optimization of 7-substituted-pyrazolo[4,3-b]pyridine ALK5 (activin receptor-like kinase 5) inhibitors.

Sabat, M., Wang, H., Scorah, N., Lawson, J.D., Atienza, J., Kamran, R., Hixon, M.S., Dougan, D.R.

(2017) Bioorg Med Chem Lett 27: 1955-1961

• PubMed: 28359790 
• DOI: https://doi.org/10.1016/j.bmcl.2017.03.026
• Primary Citation Related Structures: 
  5USQ


• PubMed Abstract: 
  

  A series of potent ALK5 inhibitors were designed using a SBDD approach and subsequently optimized to improve drug likeness. Starting with a 4-substituted quinoline screening hit, SAR was conducted using a ALK5 binding model to understand the binding site and optimize activity. The resulting inhibitors displayed excellent potency but were limited by high in vitro clearance in rat and human microsomes. Using a scaffold morphing strategy, these analogs were transformed into a related pyrazolo[4,3-b]pyridine series with improved ADME properties.

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Organizational Affiliation: 
• Takeda California, 10410 Science Center Drive, San Diego, CA 92121, United States. Electronic address: [e-mail].
Takeda California, 10410 Science Center Drive, San Diego, CA 92121, United States.

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: 34.7 kDa 
• Atom Count: 2,545 
• Modeled Residue Count: 299 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-1	A	299	Homo sapiens	Mutation(s): 0  Gene Names: TGFBR1, ALK5, SKR4 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8LY	B [auth A]	N-[2-(5-chloro-2-fluorophenyl)pyridin-4-yl]-2-[(piperidin-4-yl)methyl]-2H-pyrazolo[4,3-b]pyridin-7-amine C23 H22 Cl F N6 QZJHLQYMHQMSIQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.231 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.589	α = 90
b = 78.33	β = 90
c = 90.712	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Dougan, D.R., Lawson, J.D.

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2017-04-26
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Refinement description