5XYZ

Target information

RCSB PDB
5XYZ
Title
The structure of human BTK kinase domain in complex with a covalent inhibitor
Method
X-RAY DIFFRACTION
Resolution
2.64
Classification
TRANSFERASE/TRANSFERASE INHIBITOR
Organism
Homo sapiens
Protein
Tyrosine-protein kinase BTK (Q06187)    Looking for covalent inhibitors of this target ?
Year
2017
Publication Title
In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery.
Abstract

To explore novel kinase hinge-binding scaffolds, we carried out structure-based virtual screening against p38?? MAPK as a model system. With the assistance of developed kinase-specific structural filters, we identify a novel lead compound that selectively inhibits a panel of kinases with threonine as the gatekeeper residue, including BTK and LCK. These kinases play important roles in lymphocyte activation, which encouraged us to design novel kinase inhibitors as drug candidates for ameliorating inflammatory diseases and cancers. Therefore, we chemically modified our substituted triazole-class lead compound to improve the binding affinity and selectivity via a 'minimal decoration' strategy, which resulted in potent and selective kinase inhibitors against LCK (18 nM) and BTK (8 nM). Subsequent crystallographic experiments validated our design. These rationally designed compounds exhibit potent on-target inhibition against BTK in B cells or LCK in T cells, respectively. Our work demonstrates that structure-based virtual screening can be applied to facilitate the development of novel chemical entities in crowded chemical space in the field of kinase inhibitor discovery.

External Link
RCSB PDB





Ligand information

HET
GYL
Chain ID
A
HET Number
701
Molecular Formula
C18H15ClFN5O
Structure
2D structure
IUPAC Name
N-[3-[5-[(2-chloro-6-fluoro-phenyl)methylamino]-4H-1,2,4-triazol-3-yl]phenyl]prop-2-enamide
InChI
InChI=1S/C18H15ClFN5O/c1-2-16(26)22-12-6-3-5-11(9-12)17-23-18(25-24-17)21-10-13-14(19)7-4-8-15(13)20/h2-9H,1,10H2,(H,22,26)(H2,21,23,24,25)
InChI Key
YFVRNHCFDWIILZ-UHFFFAOYSA-N
Canonical SMILES
C=CC(=O)Nc1cccc(-c2nnc(NCc3c(F)cccc3Cl)[nH]2)c1

Covalent Binding

Warhead
Michael Acceptor
Reaction Mechanism
Michael Addition
Residue
CYS : 481
Residue Chain
A
Interactions
Pharmacophore Model