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

  • Resolution: 2.05 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK283Homo sapiensMutation(s): 4 
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
GTEx:  ENSG00000010671 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2V1

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • 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
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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