4YHF

Bruton's tyrosine kinase in complex with a t-butyl cyanoacrylamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Prolonged and tunable residence time using reversible covalent kinase inhibitors.

Bradshaw, J.M.McFarland, J.M.Paavilainen, V.O.Bisconte, A.Tam, D.Phan, V.T.Romanov, S.Finkle, D.Shu, J.Patel, V.Ton, T.Li, X.Loughhead, D.G.Nunn, P.A.Karr, D.E.Gerritsen, M.E.Funk, J.O.Owens, T.D.Verner, E.Brameld, K.A.Hill, R.J.Goldstein, D.M.Taunton, J.

(2015) Nat Chem Biol 11: 525-531

  • DOI: 10.1038/nchembio.1817
  • Primary Citation of Related Structures:  
    4YHF

  • PubMed Abstract: 
  • Drugs with prolonged on-target residence times often show superior efficacy, yet general strategies for optimizing drug-target residence time are lacking. Here we made progress toward this elusive goal by targeting a noncatalytic cysteine in Bruton's tyrosine kinase (BTK) with reversible covalent inhibitors ...

    Drugs with prolonged on-target residence times often show superior efficacy, yet general strategies for optimizing drug-target residence time are lacking. Here we made progress toward this elusive goal by targeting a noncatalytic cysteine in Bruton's tyrosine kinase (BTK) with reversible covalent inhibitors. Using an inverted orientation of the cysteine-reactive cyanoacrylamide electrophile, we identified potent and selective BTK inhibitors that demonstrated biochemical residence times spanning from minutes to 7 d. An inverted cyanoacrylamide with prolonged residence time in vivo remained bound to BTK for more than 18 h after clearance from the circulation. The inverted cyanoacrylamide strategy was further used to discover fibroblast growth factor receptor (FGFR) kinase inhibitors with residence times of several days, demonstrating the generalizability of the approach. Targeting of noncatalytic cysteines with inverted cyanoacrylamides may serve as a broadly applicable platform that facilitates 'residence time by design', the ability to modulate and improve the duration of target engagement in vivo.


    Organizational Affiliation

    Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTKA, B278Homo sapiensMutation(s): 0 
Gene Names: BTKAGMX1ATKBPK
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4C9
Query on 4C9

Download Ideal Coordinates CCD File 
C [auth A], V [auth B](2S)-2-({(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}carbonyl)-4,4-dimethylpentanenitrile
C30 H33 N7 O2
DZSBLWYJPNCWLI-FGZHOGPDSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
N [auth A], O [auth A], PA [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
JA [auth B], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], NA [auth B], OA [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
P [auth A], Q [auth A], QA [auth B], R [auth A], RA [auth B], SA [auth B], TA [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , D [auth A] , DA [auth B] , E [auth A] , EA [auth B] , F [auth A] , 
AA [auth B],  BA [auth B],  CA [auth B],  D [auth A],  DA [auth B],  E [auth A],  EA [auth B],  F [auth A],  FA [auth B],  G [auth A],  GA [auth B],  H [auth A],  HA [auth B],  I [auth A],  IA [auth B],  J [auth A],  K [auth A],  S [auth A],  T [auth B],  U [auth B],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.77α = 90
b = 77.09β = 96.43
c = 88.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesGM071434
National Institutes of HealthUnited StatesF32GM087052
Academy of FinlandFinland--
Sigrid Juselius FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 1.3: 2015-07-01
    Changes: Database references
  • Version 1.4: 2019-04-24
    Changes: Data collection, Source and taxonomy