4OT6 | pdb_00004ot6

Crystal structure of BTK kinase domain complexed with 4-Methanesulfonyl-N-(3-{8-[4-(morpholine-4-carbonyl)-phenylamino]-imidazo[1,2-a]pyrazin-6-yl}-phenyl)-benzamide

• PDB DOI: https://doi.org/10.2210/pdb4OT6/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-02-13 Released: 2014-05-14 
• Deposition Author(s): Kuglstatter, A., Wong, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.278 (Depositor), 0.322 (DCC) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Drug Design of RN486, a Potent and Selective Bruton's Tyrosine Kinase (BTK) Inhibitor, for the Treatment of Rheumatoid Arthritis.

Lou, Y., Han, X., Kuglstatter, A., Kondru, R.K., Sweeney, Z.K., Soth, M., McIntosh, J., Litman, R., Suh, J., Kocer, B., Davis, D., Park, J., Frauchiger, S., Dewdney, N., Zecic, H., Taygerly, J.P., Sarma, K., Hong, J., Hill, R.J., Gabriel, T., Goldstein, D.M., Owens, T.D.

(2015) J Med Chem 58: 512-516

• PubMed: 24712864 
• DOI: https://doi.org/10.1021/jm500305p
• Primary Citation Related Structures: 
  4OT5, 4OT6, 4OTQ, 4OTR


• PubMed Abstract: 
  

  Structure-based drug design was used to guide the optimization of a series of selective BTK inhibitors as potential treatments for Rheumatoid arthritis. Highlights include the introduction of a benzyl alcohol group and a fluorine substitution, each of which resulted in over 10-fold increase in activity. Concurrent optimization of drug-like properties led to compound 1 (RN486) ( J. Pharmacol. Exp. Ther. 2012 , 341 , 90 ), which was selected for advanced preclinical characterization based on its favorable properties.

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Organizational Affiliation: 
• pRED, Pharma Research & Early Development, Small Molecule Research, Discovery Chemistry, Hoffmann-La Roche Inc. , 3431 Hillview Avenue, Palo Alto, California 94304, 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: 33.12 kDa 
• Atom Count: 2,331 
• Modeled Residue Count: 265 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A	283	Homo sapiens	Mutation(s): 4  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 GTEx:  ENSG00000010671

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2V1	B [auth A]	4-(methylsulfonyl)-N-[3-(8-{[4-(morpholin-4-ylcarbonyl)phenyl]amino}imidazo[1,2-a]pyrazin-6-yl)phenyl]benzamide C31 H28 N6 O5 S LFFYDKBUCGOOED-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.278 (Depositor), 0.322 (DCC) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.825	α = 90
b = 105.389	β = 90
c = 38.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Kuglstatter, A., Wong, A.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2015-01-21
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description