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9zlm

Crystal structure of BTK kinase domain bound to compound YS2

Method: X-RAY DIFFRACTION D_max: 64.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zlm
deposition_date	2025-12-08
title	Crystal structure of BTK kinase domain bound to compound YS2
keywords	inhibitor, kinase, complex, 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	20.02 Å
rg_electron	18.91 Å
i0	17180700.00
molecular_weight	31694.0 kDa
excluded_volume	39790 Å³
envelope_volume	45788 Å³
shell_volume	20110 Å³
envelope_diameter	67.9 Å
shell_rg	25.44 Å
envelope_rg	19.24 Å
shape_rg	18.91 Å
total_rg	19.85 Å
total_atoms	4397
n_residues	270
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	64.7 Å
rg_real	19.94 Å
rg_real_error	0.44 Å
i0_real	1.7180e+07
i0_real_error	2.2680e+05
rg_reciprocal	19.96 Å
i0_reciprocal	17180000.0000
total_estimate	0.8092
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	25.0 Å
skewness	0.238
kurtosis	-0.352
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	5694000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	4864

KNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIREGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLPRPHLASERVYTIMYSCWHEKADERPSFKILLSNILDVMDEES

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 non-polymer

description	N-[4-(3-{2-oxo-2-[3-(phenoxymethyl)azetidin-1-yl]acetamido}phenyl)oxan-4-yl]propanamide
formula_weight	465.5 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	293

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6. Citations (1)

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length_a	71.970 Å
length_b	103.943 Å
length_c	37.973 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	1.270 Å
resolution_low	37.970 Å
r_factor	0.1990
r_work	0.1983
r_free	0.2125

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

Crystal structure of BTK kinase domain bound to compound YS2

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