9T1T | pdb_00009t1t

Crystal Structure of the correct enantiomer bound to the PH domain of Btk

PDB DOI: https://doi.org/10.2210/pdb9T1T/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-10-22 Released: 2026-11-04
Deposition Author(s): Brear, P., West, R.M., Nicolescu, R.C.B., Blaszczyk, B.K., Deingruber, T., Sanders, M.G., Perez-Areales, F.J., Spring, D.R., Hyvonen, M.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.367 (Depositor), 0.331 (DCC)
R-Value Work:
0.296 (Depositor), 0.285 (DCC)
R-Value Observed:
0.299 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Inhibition of a Pleckstrin Homology Domain by Lysine-reactive Covalent Inhibitor

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

To be published.

Macromolecule Content

Total Structure Weight: 80.53 kDa
Atom Count: 5,510
Modeled Residue Count: 640
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A, B [auth C], C [auth G], D [auth J]	169	Homo sapiens	Mutation(s): 1 Gene Names: BTK, AGMX1, ATK, BPK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Go to UniProtKB: Q06187
PHAROS: Q06187 GTEx: ENSG00000010671
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06187-2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JS0 (Subject of Investigation/LOI) Query on A1JS0 Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	(6~{R})-6-(2-bromanyl-6-chloranyl-phenyl)-4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid C₁₅ H₁₂ Br Cl O₃ PXATWEDKSIVULN-MRVPVSSYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] SDF format, chain K [auth J] SDF format, chain I [auth G] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain K [auth J] MOL2 format, chain I [auth G] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain K [auth J] mmCIF format, chain I [auth G]	E [auth A], H [auth C], I [auth G], K [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Focus chain I [auth G] Focus chain K [auth J] Interactions & Density Focus chain E [auth A] Focus chain H [auth C] Focus chain I [auth G] Focus chain K [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth G] MOL2 format, chain F [auth A] MOL2 format, chain J [auth G] mmCIF format, chain F [auth A] mmCIF format, chain J [auth G]	F [auth A], J [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth G] Interactions & Density Focus chain F [auth A] Focus chain J [auth G]