6YYG

Crystal Structure of 5-(trifluoromethoxy)indoline-2,3-dione covalently bound to the PH domain of Bruton's tyrosine kinase mutant R28C

PDB DOI: https://doi.org/10.2210/pdb6YYG/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-05 Released: 2021-05-12
Deposition Author(s): Brear, P., Wagstaff, J., Hyvonen, M.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.299
R-Value Work: 0.230
R-Value Observed: 0.234

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Optimising crystallographic systems for structure-guided drug discovery

Brear, P., Fischer, G., May, M., Pantelejevs, T., Mathieu, R., Rossmann, M., Wagstaff, J., Blaszczyk, B., Hyvonen, M.

To be published.

Macromolecule Content

Total Structure Weight: 80.89 kDa
Atom Count: 5,487
Modelled Residue Count: 624
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A, B, C, D	169	Homo sapiens	Mutation(s): 0 Gene Names: BTK, AGMX1, ATK, BPK 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06187
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q1B (Subject of Investigation/LOI) Query on Q1B Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D]	E [auth A], H [auth B], K [auth D]	5-(trifluoromethyloxy)-1,3-dihydroindol-2-one C₉ H₆ F₃ N O₂ NJZFZLIOCDIELL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D]	G [auth A], I [auth B], J [auth C], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain M [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth D]	F [auth A], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth D]