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9y9n

;PLK4 in complex with Compound 25 ((R)-7-hydroxy-N-(3-(1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl)-1H-pyrazol-4-yl)-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide) ;

Method: X-RAY DIFFRACTION D_max: 62.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y9n
deposition_date	2025-09-14
last_revision	2026-02-18
title	;PLK4 in complex with Compound 25 ((R)-7-hydroxy-N-(3-(1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl)-1H-pyrazol-4-yl)-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide) ;
keywords	PLK4, type 1 inhibitor, SBDD, 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	19.51 Å
rg_electron	18.63 Å
i0	12392000.00
molecular_weight	26470.0 kDa
excluded_volume	33130 Å³
envelope_volume	38076 Å³
shell_volume	17488 Å³
envelope_diameter	64.4 Å
shell_rg	24.46 Å
envelope_rg	18.92 Å
shape_rg	18.67 Å
total_rg	19.37 Å
total_atoms	3681
n_residues	226
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	62.9 Å
rg_real	19.50 Å
rg_real_error	0.46 Å
i0_real	1.2390e+07
i0_real_error	1.4670e+05
rg_reciprocal	19.50 Å
i0_reciprocal	12390000.0000
total_estimate	0.8104
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.0 Å
skewness	0.361
kurtosis	-0.291
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	3508000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Serine/threonine-protein kinase PLK4
formula_weight	30530.4 kDa
ec_number	2.7.11.21
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3834

CIGEKIEDFKVGNLLGKGSFAGVYRAESIHTGLEVAIKMIDKKAMYKAGMVQRVQNEVKIHCQLKHPSILELYNYFEDSNYVYLVLEMCHNGEMNRYLKNRVKPFSENEARHFMHQIITGMLYLHSHGILHRDLTLSNLLLTRNMNIKIADFGLATQLKMPHEKHYDLCGTPNYISPEIATRSAHGLESDVWSLGCMFYTLLIGRPPFDTDTVKNTLNKVVLADYEMPSFLSIEAKDLIHQLLRRNPADRLSLSSVLDHPFMSRNS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;(7R)-7-hydroxy-N-{(5P)-5-[1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-1H-pyrazol-4-yl}-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide ;
formula_weight	503.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	128

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6. Citations (1)

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length_a	105.097 Å
length_b	105.097 Å
length_c	47.974 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	—

resolution	1.810 Å
resolution_low	23.200 Å
r_factor	0.2094
r_work	0.2080
r_free	0.2372

fit	/app/data/saxs_computation/y9/9y9n/9y9n.fit
pddf	/app/data/pr_computation/y9/9y9n/9y9n.pr.out
profile	/app/data/saxs_computation/y9/9y9n/9y9n.dat

;PLK4 in complex with Compound 25 ((R)-7-hydroxy-N-(3-(1-(2,2,2-trifluoroethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl)-1H-pyrazol-4-yl)-7-(trifluoromethyl)-4-azaspiro[2.5]octane-4-carboxamide) ;

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