← Back to search

9y9b

PLK4 in complex with Compound 6 (3-hydroxy-N-(3-(pyridin-2-yl)-1H-pyrazol-4-yl)-8-azabicyclo[3.2.1]octane-8-carboxamide)

Method: X-RAY DIFFRACTION D_max: 64.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y9b
deposition_date	2025-09-13
last_revision	2026-02-18
title	PLK4 in complex with Compound 6 (3-hydroxy-N-(3-(pyridin-2-yl)-1H-pyrazol-4-yl)-8-azabicyclo[3.2.1]octane-8-carboxamide)
keywords	PLK4, type 1 inhibitor, SBDD, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	19.98 Å
rg_electron	19.21 Å
i0	24311900.00
molecular_weight	25233.0 kDa
excluded_volume	24479 Å³
envelope_volume	40418 Å³
shell_volume	18046 Å³
envelope_diameter	67.4 Å
shell_rg	25.00 Å
envelope_rg	19.43 Å
shape_rg	19.14 Å
total_rg	19.98 Å
total_atoms	1923
n_residues	233
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

▼

3. P(r) Analysis (GNOM)

dmax	64.5 Å
rg_real	19.97 Å
rg_real_error	0.35 Å
i0_real	2.4310e+07
i0_real_error	2.7720e+05
rg_reciprocal	19.97 Å
i0_reciprocal	24310000.0000
total_estimate	0.8170
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.7 Å
skewness	0.362
kurtosis	-0.350
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	5397000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Serine/threonine-protein kinase PLK4
formula_weight	31723.7 kDa
ec_number	2.7.11.21
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1953

SLATCIGEKIEDFKVGNLLGKGSFAGVYRAESIHTGLEVAIKMIDKKAMYKAGMVQRVQNEVKIHCQLKHPSILELYNYFEDSNYVYLVLEMCHNGEMNRYLKNRVKPFSENEARHFMHQIITGMLYLHSHGILHRDLTLSNLLLTRNMNIKIADFGLATQLKMPHEKHYTLCGTPNYISPEIATRSAHGLESDVWSLGCMFYTLLIGRPPFDTDTVKNTLNKVVLADYEMPSFLSIEAKDLIHQLLRRNPADRLSLSSVLDHPFMSRNSSTKSKDEG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	(1R,3r,5S)-3-hydroxy-N-[3-(pyridin-2-yl)-1H-pyrazol-4-yl]-8-azabicyclo[3.2.1]octane-8-carboxamide
formula_weight	313.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	22

▶

6. Citations (1)

▶

length_a	62.333 Å
length_b	83.991 Å
length_c	43.030 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	2.700 Å
resolution_low	29.220 Å
r_factor	0.2451
r_work	0.2405
r_free	0.3345

fit	/app/data/saxs_computation/y9/9y9b/9y9b.fit
pddf	/app/data/pr_computation/y9/9y9b/9y9b.pr.out
profile	/app/data/saxs_computation/y9/9y9b/9y9b.dat

PLK4 in complex with Compound 6 (3-hydroxy-N-(3-(pyridin-2-yl)-1H-pyrazol-4-yl)-8-azabicyclo[3.2.1]octane-8-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