7N5X | pdb_00007n5x

Fragment-Based Discovery of a Novel Bruton's Tyrosine Kinase Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.188 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.166 (Depositor) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of the Bruton's Tyrosine Kinase Inhibitor Clinical Candidate TAK-020 ( S )-5-(1-((1-Acryloylpyrrolidin-3-yl)oxy)isoquinolin-3-yl)-2,4-dihydro-3 H -1,2,4-triazol-3-one, by Fragment-Based Drug Design.

Sabat, M.Dougan, D.R.Knight, B.Lawson, J.D.Scorah, N.Smith, C.R.Taylor, E.R.Vu, P.Wyrick, C.Wang, H.Balakrishna, D.Hixon, M.Madakamutil, L.McConn, D.

(2021) J Med Chem 64: 12893-12902

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01026
  • Primary Citation Related Structures: 
    7N5O, 7N5R, 7N5X, 7N5Y

  • PubMed Abstract: 

    This publication details the successful use of FBDD (fragment-based drug discovery) principles in the invention of a novel covalent Bruton's tyrosine kinase inhibitor, which ultimately became the Takeda Pharmaceuticals clinical candidate TAK-020. Described herein are the discovery of the fragment 5-phenyl-2,4-dihydro-3 H -1,2,4-triazol-3-one, the subsequent optimization of this hit molecule to the candidate, and synthesis and performance in pharmacodynamic and efficacy models along with direct biophysical comparison of TAK-020 with other clinical-level assets and the marketed drug Ibrutinib.


  • Organizational Affiliation
    • Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States.

Macromolecule Content 

  • Total Structure Weight: 33.25 kDa 
  • Atom Count: 2,535 
  • Modeled Residue Count: 269 
  • Deposited Residue Count: 283 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK283Homo 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
GTEx:  ENSG00000010671 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0GW
(Subject of Investigation/LOI)

Query on 0GW



Download:Ideal Coordinates CCD File
F [auth A]5-(1-ethoxyisoquinolin-3-yl)-2,4-dihydro-3H-1,2,4-triazol-3-one
C13 H12 N4 O2
RHTTUBBYQVKYBV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
PGO

Query on PGO



Download:Ideal Coordinates CCD File
C [auth A]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
B [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
0GW BindingDB:  7N5X IC50: 50 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.188 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.166 (Depositor) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.758α = 90
b = 104.883β = 90
c = 38.054γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description