6TUH | pdb_00006tuh

PH domain of Bruton's tyrosine kinase bound to compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6TUH

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Targeting a Pleckstrin Homology Domain with a Lysine-Reactive Covalent Binder.

West, R.M.Bizga Nicolescu, R.C.Brear, P.Wagstaff, J.Blaszczyk, B.K.Deingruber, T.Sanders, M.G.Perez-Areales, F.J.Spring, D.R.Hyvonen, M.

(2026) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c03818
  • Primary Citation Related Structures: 
    6TUH, 9RL9, 9RMO, 9T23, 9T3M

  • PubMed Abstract: 

    Bruton's Tyrosine Kinase (BTK) is a validated target for hematological malignancies, with numerous FDA-approved inhibitors on the market. Current therapies target the highly conserved ATP binding site and hence limit the therapeutic index given the site's highly conserved nature across the kinome. We explore a novel approach for BTK inhibition by targeting the PH domain-mediated membrane recruitment and activation of BTK. We have identified a fragment which covalently modifies a lysine in the inositol phosphate (PIP3) binding site and inhibits the binding of a soluble PIP3 headgroup analog to the PH domain. Fragment growth and an extensive structure-binding relationship study uncovered 27 crystal structures and a best-in-class analog, 24 . Evaluation of p K a values of the targeted lysine in BTK and other PH domains suggests this as a more general approach to PH domain inhibition.


  • Organizational Affiliation
    • Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.

Macromolecule Content 

  • Total Structure Weight: 80.98 kDa 
  • Atom Count: 5,181 
  • Modeled Residue Count: 607 
  • Deposited Residue Count: 676 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK
A, B, C, D
169Homo sapiensMutation(s): 1 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXT
(Subject of Investigation/LOI)

Query on NXT



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth B],
K [auth C],
M [auth D]
4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid
C9 H10 O3
QQPMDRGNNFKVEL-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
L [auth C],
N [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.759α = 90
b = 66.606β = 100.06
c = 80.267γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Advisory, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2026-05-20
    Changes: Database references