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9ugf

CDK2 small molecule F05

Method: X-RAY DIFFRACTION D_max: 66.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ugf
deposition_date	2025-04-11
last_revision	2026-04-15
title	CDK2 small molecule F05
keywords	inhibitor, CELL CYCLE; CELL CYCLE
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	20.32 Å
rg_electron	19.49 Å
i0	30931600.00
molecular_weight	29618.0 kDa
excluded_volume	29273 Å³
envelope_volume	47236 Å³
shell_volume	20354 Å³
envelope_diameter	67.8 Å
shell_rg	25.82 Å
envelope_rg	19.72 Å
shape_rg	19.42 Å
total_rg	20.29 Å
total_atoms	2292
n_residues	277
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	66.8 Å
rg_real	20.27 Å
rg_real_error	0.41 Å
i0_real	3.0930e+07
i0_real_error	3.9570e+05
rg_reciprocal	20.28 Å
i0_reciprocal	30930000.0000
total_estimate	0.8881
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.9 Å
skewness	0.305
kurtosis	-0.319
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	7660000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Cyclin-dependent kinase 2
formula_weight	34387.9 kDa
ec_number	2.7.11.22
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2476

GPLGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;2-[(1-methylsulfonylpiperidin-4-yl)amino]-8-[1-[[1-[(1~{S})-2-oxidanyl-1-phenyl-ethyl]-1,2,3-triazol-4-yl]methyl]piperidin-4-yl]pyrido[2,3-d]pyrimidin-7-one ;
formula_weight	607.7 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	178

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6. Citations (1)

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length_a	53.705 Å
length_b	72.139 Å
length_c	72.195 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.640 Å
resolution_low	43.090 Å
r_factor	0.2139
r_work	0.2118
r_free	0.2523

fit	/app/data/saxs_computation/ug/9ugf/9ugf.fit
pddf	/app/data/pr_computation/ug/9ugf/9ugf.pr.out
profile	/app/data/saxs_computation/ug/9ugf/9ugf.dat

CDK2 small molecule F05

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