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: 32.81 kDa 
• Atom Count: 2,638 
• Modelled Residue Count: 265 
• Deposited Residue Count: 271 
• Unique protein chains: 1

 4RX5

Bruton's tyrosine kinase (BTK) with pyridazinone compound 23

• PDB DOI:  https://doi.org/10.2210/pdb4RX5/pdb

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


• Deposited: 2014-12-08 Released: 2015-12-02 
• Deposition Author(s): Eigenbrot, C., Yu, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.179 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

Discovery of highly potent and selective Bruton's tyrosine kinase inhibitors: Pyridazinone analogs with improved metabolic stability.

Young, W.B., Barbosa, J., Blomgren, P., Bremer, M.C., Crawford, J.J., Dambach, D., Eigenbrot, C., Gallion, S., Johnson, A.R., Kropf, J.E., Lee, S.H., Liu, L., Lubach, J.W., Macaluso, J., Maciejewski, P., Mitchell, S.A., Ortwine, D.F., Di Paolo, J., Reif, K., Scheerens, H., Schmitt, A., Wang, X., Wong, H., Xiong, J.M., Xu, J., Yu, C., Zhao, Z., Currie, K.S.

(2016) Bioorg Med Chem Lett 26: 575-579

• PubMed: 26675441 
• DOI: https://doi.org/10.1016/j.bmcl.2015.11.076
• Primary Citation of Related Structures:  
  4RX5


• PubMed Abstract: 
  

BTK inhibitor GDC-0834 (1) was found to be rapidly metabolized in human studies, resulting in a suspension of clinical trials. The primary route of metabolism was through cleavage of the acyclic amide bond connecting the terminal tetrahydrobenzothiophene with the central linker aryl ring. SAR studies were focused on reducing metabolic cleavage of this amide, and resulted in the identification of several central aryl linker substituents that conferred improved stability. The most promising substituted aryl linkers were then incorporated into an optimized pyridazinone scaffold, resulting in the identification of lead analog 23, possessing improved potency, metabolic stability and preclinical properties.

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Organizational Affiliation: 

Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A	271	Homo sapiens	Mutation(s): 0  Gene Names: BTK, AGMX1, ATK, BPK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Explore Q06187  Go to UniProtKB:  Q06187
PHAROS:  Q06187

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3YO	G [auth A]	N-(6-fluoro-2-methyl-3-{5-[(5-methyl-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-2-yl)amino]-6-oxo-1,6-dihydropyridazin-3-yl}phenyl)-1-benzothiophene-2-carboxamide C27 H24 F N7 O2 S MZSDTUIZKGUVHK-UHFFFAOYSA-N
PG0	F [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3YO	BindingDB:  4RX5	IC50: min: 3, max: 91 (nM) from 2 assay(s)
	Binding MOAD:  4RX5	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.179 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.3	α = 90
b = 108.3	β = 90
c = 42.422	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Eigenbrot, C., Yu, C.

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Database references