5U9D

Discovery of a potent BTK inhibitor with a novel binding mode using parallel selections with a DNA-encoded chemical library


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of a Potent BTK Inhibitor with a Novel Binding Mode by Using Parallel Selections with a DNA-Encoded Chemical Library.

Cuozzo, J.W.Centrella, P.A.Gikunju, D.Habeshian, S.Hupp, C.D.Keefe, A.D.Sigel, E.A.Soutter, H.H.Thomson, H.A.Zhang, Y.Clark, M.A.

(2017) Chembiochem 18: 864-871

  • DOI: 10.1002/cbic.201600573

  • PubMed Abstract: 
  • We have identified and characterized novel potent inhibitors of Bruton's tyrosine kinase (BTK) from a single DNA-encoded library of over 110 million compounds by using multiple parallel selection conditions, including variation in target concentratio ...

    We have identified and characterized novel potent inhibitors of Bruton's tyrosine kinase (BTK) from a single DNA-encoded library of over 110 million compounds by using multiple parallel selection conditions, including variation in target concentration and addition of known binders to provide competition information. Distinct binding profiles were observed by comparing enrichments of library building block combinations under these conditions; one enriched only at high concentrations of BTK and was competitive with ATP, and another enriched at both high and low concentrations of BTK and was not competitive with ATP. A compound representing the latter profile showed low nanomolar potency in biochemical and cellular BTK assays. Results from kinetic mechanism of action studies were consistent with the selection profiles. Analysis of the co-crystal structure of the most potent compound demonstrated a novel binding mode that revealed a new pocket in BTK. Our results demonstrate that profile-based selection strategies using DNA-encoded libraries form the basis of a new methodology to rapidly identify small molecule inhibitors with novel binding modes to clinically relevant targets.


    Organizational Affiliation

    X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase BTK
A
271Homo sapiensMutation(s): 0 
Gene Names: BTK (AGMX1, ATK, BPK)
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Go to Gene View: BTK
Go to UniProtKB:  Q06187
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
83P
Query on 83P

Download SDF File 
Download CCD File 
A
(R)-N-methyl-2-(3-((quinoxalin-6-ylamino)methyl)furan-2-carbonyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide
(3R)-N-methyl-2-(3-{[(quinoxalin-6-yl)amino]methyl}furan-2-carbonyl)-2,3,4,9-tetrahydro-1H-beta-carboline-3-carboxamide
C27 H24 N6 O3
WHELPQVBBOUXAO-XMMPIXPASA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.553α = 90.00
b = 103.483β = 90.00
c = 37.839γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-05-10
    Type: Database references