7KXQ | pdb_00007kxq

BTK1 SOAKED WITH COMPOUND 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 
    0.182 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7KXQ

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of potent and selective reversible Bruton's tyrosine kinase inhibitors.

Qiu, H.Ali, Z.Bender, A.Caldwell, R.Chen, Y.Y.Fang, Z.Gardberg, A.Glaser, N.Goettsche, A.Goutopoulos, A.Grenningloh, R.Hanschke, B.Head, J.Johnson, T.Jones, C.Jones, R.Kulkarni, S.Maurer, C.Morandi, F.Neagu, C.Poetzsch, S.Potnick, J.Schmidt, R.Roe, K.Viacava Follis, A.Wing, C.Zhu, X.Sherer, B.

(2021) Bioorg Med Chem 40: 116163-116163

  • DOI: https://doi.org/10.1016/j.bmc.2021.116163
  • Primary Citation Related Structures: 
    7KXL, 7KXM, 7KXN, 7KXO, 7KXP, 7KXQ

  • PubMed Abstract: 

    Bruton's tyrosine kinase (BTK) is a cytoplasmic, non-receptor tyrosine kinase member of the TEC family of tyrosine kinases. Pre-clinical and clinical data have shown that targeting BTK can be used for the treatment for B-cell disorders. Here we disclose the discovery of a novel imidazo[4,5-b]pyridine series of potent, selective reversible BTK inhibitors through a rational design approach. From a starting hit molecule 1, medicinal chemistry optimization led to the development of a lead compound 30, which exhibited 58 nM BTK inhibitory potency in human whole blood and high kinome selectivity. Additionally, the compound demonstrated favorable pharmacokinetics (PK), and showed potent dose-dependent efficacy in a rat CIA model.


  • Organizational Affiliation
    • EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1). Electronic address: hui.qiu@emdserono.com.

Macromolecule Content 

  • Total Structure Weight: 32.26 kDa 
  • Atom Count: 2,621 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 270 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform BTK-C of Tyrosine-protein kinase BTK270Homo sapiensMutation(s): 0 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X9Y
(Subject of Investigation/LOI)

Query on X9Y



Download:Ideal Coordinates CCD File
D [auth A]3-tert-butyl-N-[(5R)-2-{2-[3,5-dimethyl-1-(propan-2-yl)-1H-pyrazol-4-yl]-3H-imidazo[4,5-b]pyridin-7-yl}-6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-yl]-1,2,4-oxadiazole-5-carboxamide
C32 H38 N8 O2
XHKFYFCKCXKVPO-XMMPIXPASA-N
DMS

Query on DMS



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free:  0.182 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.514α = 90
b = 103.045β = 90
c = 38.453γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description