7L5P

Crystal structure of the covalently bonded complex of rilzabrutinib with BTK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted R1LClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

The Discovery Rilzabrutinib (PRN1008): A Reversible Covalent BTK Inhibitor for Immune Mediated Diseases

Owens, T.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK
A, B
271Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R1L (Subject of Investigation/LOI)
Query on R1L

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
(2E)-2-{(3R)-3-[4-amino-3-(2-fluoro-4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidine-1-carbonyl}-4-methyl-4-[4-(oxetan-3-yl)piperazin-1-yl]pent-2-enenitrile
C36 H40 F N9 O3
LCFFREMLXLZNHE-GBOLQPHISA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
R1L BindingDB:  7L5P IC50: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.81α = 90
b = 76.684β = 96.46
c = 88.321γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted R1LClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary