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9yki

Crystal structure of human PIM1 kinase bound with CSH-4044 inhibitor

Method: X-RAY DIFFRACTION D_max: 62.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yki
deposition_date	2025-10-07
title	Crystal structure of human PIM1 kinase bound with CSH-4044 inhibitor
keywords	Kinase, Inhibitor, Co-crystallization, TRANSFERASE; TRANSFERASE
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	19.86 Å
rg_electron	18.92 Å
i0	33376700.00
molecular_weight	29864.0 kDa
excluded_volume	28898 Å³
envelope_volume	45683 Å³
shell_volume	20118 Å³
envelope_diameter	64.1 Å
shell_rg	25.29 Å
envelope_rg	19.09 Å
shape_rg	18.90 Å
total_rg	19.60 Å
total_atoms	2265
n_residues	273
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	62.1 Å
rg_real	19.76 Å
rg_real_error	0.24 Å
i0_real	3.3380e+07
i0_real_error	4.3320e+05
rg_reciprocal	19.77 Å
i0_reciprocal	33380000.0000
total_estimate	0.7195
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	24.5 Å
skewness	0.236
kurtosis	-0.397
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	7154000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.210; Positv: 1.000; Valcen: 0.999; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Serine/threonine-protein kinase pim-1
formula_weight	35812.7 kDa
ec_number	2.7.11.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2450

MLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2,5-dihydroxy-4-methoxyphenyl)(6-hydroxy-5-methoxy-1,3-benzothiazol-2-yl)methanone
formula_weight	347.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	177

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6. Citations (1)

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length_a	97.930 Å
length_b	97.930 Å
length_c	80.404 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 65
int_tables_number	170
crystal_system	hexagonal

resolution	1.950 Å
resolution_low	41.820 Å
r_factor	0.1626
r_work	0.1610
r_free	0.1927

fit	/app/data/saxs_computation/yk/9yki/9yki.fit
pddf	/app/data/pr_computation/yk/9yki/9yki.pr.out
profile	/app/data/saxs_computation/yk/9yki/9yki.dat