Crystal structure of mouse BTK kinase domain in complex with compound 9a

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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Aminopyrazole Carboxamide Bruton's Tyrosine Kinase Inhibitors. Irreversible to Reversible Covalent Reactive Group Tuning.

Schnute, M.E.Benoit, S.E.Buchler, I.P.Caspers, N.Grapperhaus, M.L.Han, S.Hotchandani, R.Huang, N.Hughes, R.O.Juba, B.M.Kim, K.H.Liu, E.McCarthy, E.Messing, D.Miyashiro, J.S.Mohan, S.O'Connell, T.N.Ohren, J.F.Parikh, M.D.Schmidt, M.Selness, S.R.Springer, J.R.Thanabal, V.Trujillo, J.I.Walker, D.P.Wan, Z.K.Withka, J.M.Wittwer, A.J.Wood, N.L.Xing, L.Zapf, C.W.Douhan III, J.

(2019) ACS Med Chem Lett 10: 80-85

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00461
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Potent covalent inhibitors of Bruton's tyrosine kinase (BTK) based on an aminopyrazole carboxamide scaffold have been identified. Compared to acrylamide-based covalent reactive groups leading to irreversible protein adducts, cyanamide-based reversible-covalent inhibitors provided the highest combined BTK potency and EGFR selectivity. The cyanamide covalent mechanism with BTK was confirmed through enzyme kinetic, NMR, MS, and X-ray crystallographic studies. The lead cyanamide-based inhibitors demonstrated excellent kinome selectivity and rat pharmacokinetic properties.

  • Organizational Affiliation

    Medicinal Chemistry and Inflammation and Immunology Research, Pfizer, St. Louis, Missouri 63017, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase
A, B
276Mus musculusMutation(s): 0 
Gene Names: Btk
UniProt & NIH Common Fund Data Resources
Find proteins for P35991 (Mus musculus)
Explore P35991 
Go to UniProtKB:  P35991
IMPC:  MGI:88216
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35991
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JVP

Download Ideal Coordinates CCD File 
C [auth A]5-amino-1-[(3R)-1-cyanopiperidin-3-yl]-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazole-4-carboxamide
C22 H20 F2 N6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
JVP BindingDB:  6MNY IC50: min: 1.3, max: 17.3 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.945α = 76.77
b = 63.515β = 85.27
c = 70.005γ = 78.13
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALAdata 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: 2019-01-30
    Type: Initial release