9zlj

Crystal structure of BTK kinase domain bound to compound YS1

Method: X-RAY DIFFRACTION Dmax: 64.0 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tyrosine-protein kinase BTK

Mus musculus

UniProt P35991

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 382–659 Mutation:Y617P A1C20 N-{(1r,4r)-4-[2-(4-chlorophenoxy)acetamido]cyclohexyl}-N-[2-(4-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)ethyl]propanamide × 1 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;277 K;15-25% PEG3350, 0.1M imidazole Resolution 1.60 Å R-free 0.218

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BTK_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–278; UniProt 382–659

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9zlj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zlj
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id9zlj
Deposition date deposition_date2025-12-08
Structure title titleCrystal structure of BTK kinase domain bound to compound YS1
Keywords keywordsinhibitor, kinase, TRANSFERASE-TRANSFERASE INHIBITOR complex, TRANSFERASE; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.03
Radius of gyration Rg (electron density) rg_electron18.83
Forward intensity I(0) i017122800.00
Molecular weight molecular_weight31654.0 kDa
Excluded volume excluded_volume39707 ų
Envelope volume envelope_volume45342 ų
Hydration-shell volume shell_volume20010 ų
Envelope diameter envelope_diameter64.7
Shell Rg shell_rg25.32
Envelope Rg envelope_rg19.10
Shape Rg shape_rg18.79
Total Rg total_rg19.89
Total atoms total_atoms4378
Residues n_residues268
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax64.0
Rg (real space) rg_real19.94
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real1.7120e+07
I(0) uncertainty (real space) i0_real_error2.1500e+05
Rg (reciprocal space) rg_reciprocal19.96
I(0) (reciprocal space) i0_reciprocal17120000.0000
Solution quality estimate total_estimate0.8883
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6
Skewness Skewness skewness0.229
Kurtosis Kurtosis kurtosis-0.373
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5246000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.928

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)