Bruton's tyrosine kinase (BTK) with GDC-0853

Experimental Data Snapshot

  • Resolution: 1.59 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery of GDC-0853: A Potent, Selective, and Noncovalent Bruton's Tyrosine Kinase Inhibitor in Early Clinical Development.

Crawford, J.J.Johnson, A.R.Misner, D.L.Belmont, L.D.Castanedo, G.Choy, R.Coraggio, M.Dong, L.Eigenbrot, C.Erickson, R.Ghilardi, N.Hau, J.Katewa, A.Kohli, P.B.Lee, W.Lubach, J.W.McKenzie, B.S.Ortwine, D.F.Schutt, L.Tay, S.Wei, B.Reif, K.Liu, L.Wong, H.Young, W.B.

(2018) J Med Chem 61: 2227-2245

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01712
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bruton's tyrosine kinase (Btk) is a nonreceptor cytoplasmic tyrosine kinase involved in B-cell and myeloid cell activation, downstream of B-cell and Fcγ receptors, respectively. Preclinical studies have indicated that inhibition of Btk activity might offer a potential therapy in autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus. Here we disclose the discovery and preclinical characterization of a potent, selective, and noncovalent Btk inhibitor currently in clinical development. GDC-0853 (29) suppresses B cell- and myeloid cell-mediated components of disease and demonstrates dose-dependent activity in an in vivo rat model of inflammatory arthritis. It demonstrates highly favorable safety, pharmacokinetic (PK), and pharmacodynamic (PD) profiles in preclinical and Phase 2 studies ongoing in patients with rheumatoid arthritis, lupus, and chronic spontaneous urticaria. On the basis of its potency, selectivity, long target residence time, and noncovalent mode of inhibition, 29 has the potential to be a best-in-class Btk inhibitor for a wide range of immunological indications.

  • Organizational Affiliation

    Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK271Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
PHAROS:  Q06187
GTEx:  ENSG00000010671 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9AJ

Download Ideal Coordinates CCD File 
B [auth A]2-[3'-(hydroxymethyl)-1-methyl-5-({5-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-2-yl}amino)-6-oxo[1,6-dihydro[3,4'-bipyridine]]-2'-yl]-7,7-dimethyl-3,4,7,8-tetrahydro-2H-cyclopenta[4,5]pyrrolo[1,2-a]pyrazin-1(6H)-one
C37 H44 N8 O4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
9AJ Binding MOAD:  5VFI Ki: 0.91 (nM) from 1 assay(s)
BindingDB:  5VFI Ki: 0.91 (nM) from 1 assay(s)
IC50: min: 1.2, max: 31 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.59 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.867α = 90
b = 103.908β = 90
c = 38.464γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Advisory, Data collection, Database references