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9zlj

Crystal structure of BTK kinase domain bound to compound YS1

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zlj
deposition_date	2025-12-08
title	Crystal structure of BTK kinase domain bound to compound YS1
keywords	inhibitor, kinase, TRANSFERASE-TRANSFERASE INHIBITOR complex, TRANSFERASE; TRANSFERASE/TRANSFERASE INHIBITOR
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	20.03 Å
rg_electron	18.83 Å
i0	17122800.00
molecular_weight	31654.0 kDa
excluded_volume	39707 Å³
envelope_volume	45342 Å³
shell_volume	20010 Å³
envelope_diameter	64.7 Å
shell_rg	25.32 Å
envelope_rg	19.10 Å
shape_rg	18.79 Å
total_rg	19.89 Å
total_atoms	4378
n_residues	268
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	64.0 Å
rg_real	19.94 Å
rg_real_error	0.35 Å
i0_real	1.7120e+07
i0_real_error	2.1500e+05
rg_reciprocal	19.96 Å
i0_reciprocal	17120000.0000
total_estimate	0.8883
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.6 Å
skewness	0.229
kurtosis	-0.373
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	5246000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Tyrosine-protein kinase BTK
formula_weight	32245.0 kDa
ec_number	2.7.10.2
mutation	Y617P
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4946

KNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIREGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLPRPHLASERVYTIMYSCWHEKADERPSFKILLSNILDVMDEES

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 non-polymer

description	N-{(1r,4r)-4-[2-(4-chlorophenoxy)acetamido]cyclohexyl}-N-[2-(4-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)ethyl]propanamide
formula_weight	497.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	371

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6. Citations (1)

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length_a	72.024 Å
length_b	103.974 Å
length_c	38.069 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	orthorhombic

resolution	1.600 Å
resolution_low	38.070 Å
r_factor	0.1863
r_work	0.1846
r_free	0.2177

fit	/app/data/saxs_computation/zl/9zlj/9zlj.fit
pddf	/app/data/pr_computation/zl/9zlj/9zlj.pr.out
profile	/app/data/saxs_computation/zl/9zlj/9zlj.dat

Crystal structure of BTK kinase domain bound to compound YS1

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction