4OT6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1021/jm500305p
  • Primary Citation of 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 wh ...

    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.


    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK A283Homo sapiensMutation(s): 4 
Gene Names: BTKAGMX1ATKBPK
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
NIH Common Fund Data Resources
PHAROS:  Q06187
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2V1
Query on 2V1

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.825α = 90
b = 105.389β = 90
c = 38.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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