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9vfo

;Crystal Structure of the NUAK1-MARK3 kinase domain chimera bound with small molecule inhibitor 2-amino-N-(5-((5-chloro-4-(((3R,3aR,6R,6aR)-6-methoxyhexahydrofuro[3,2-b]furan-3-yl)oxy)pyrimidin-2-yl)amino)-2-((2-(dimethylamino)ethyl)(methyl)amino)phenyl)acetamide ;

Method: X-RAY DIFFRACTION D_max: 71.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vfo
deposition_date	2025-06-11
last_revision	2026-04-22
title	;Crystal Structure of the NUAK1-MARK3 kinase domain chimera bound with small molecule inhibitor 2-amino-N-(5-((5-chloro-4-(((3R,3aR,6R,6aR)-6-methoxyhexahydrofuro[3,2-b]furan-3-yl)oxy)pyrimidin-2-yl)amino)-2-((2-(dimethylamino)ethyl)(methyl)amino)phenyl)acetamide ;
keywords	kinase, 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	21.58 Å
rg_electron	20.74 Å
i0	43733900.00
molecular_weight	34343.0 kDa
excluded_volume	33285 Å³
envelope_volume	55063 Å³
shell_volume	22292 Å³
envelope_diameter	73.0 Å
shell_rg	27.33 Å
envelope_rg	20.97 Å
shape_rg	20.73 Å
total_rg	21.42 Å
total_atoms	2605
n_residues	318
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	71.5 Å
rg_real	21.54 Å
rg_real_error	0.39 Å
i0_real	4.3730e+07
i0_real_error	5.3620e+05
rg_reciprocal	21.55 Å
i0_reciprocal	43730000.0000
total_estimate	0.8851
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	70.4 Å
skewness	0.330
kurtosis	-0.293
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	8910000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	MAP/microtubule affinity-regulating kinase 3
formula_weight	37744.7 kDa
ec_number	2.7.11.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2701

MGSDEQPHIGNYRLLKTLGKGNFAKVKRARHILTGREVAIKIIDKTQLNPTSLQKLFREVRIMKILNHPNIIKLFEVIETEKTLYLIMEYASKGEVYDYLVEHGRMKEKEARSKFRQIVSAVQYCHQKRIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGGKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKRFLVLNPIKRGTLEQIMKDRWINAGHEEDELKPFVEPELDISDQKRIDIMVGMGYSQEEIQESLSKMKYDEITATYLLLGRKSSE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;N-[5-[[4-[[(3R,3aR,6R,6aR)-3-methoxy-2,3,3a,5,6,6a-hexahydrofuro[3,2-b]furan-6-yl]oxy]-5-chloranyl-pyrimidin-2-yl]amino]-2-[2-(dimethylamino)ethyl-methyl-amino]phenyl]-2-azanyl-ethanamide ;
formula_weight	536.0 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	96

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6. Citations (1)

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length_a	45.405 Å
length_b	116.184 Å
length_c	160.558 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	orthorhombic

resolution	2.500 Å
resolution_low	47.063 Å
r_factor	0.1876
r_work	0.1821
r_free	0.2371

fit	/app/data/saxs_computation/vf/9vfo/9vfo.fit
pddf	/app/data/pr_computation/vf/9vfo/9vfo.pr.out
profile	/app/data/saxs_computation/vf/9vfo/9vfo.dat

;Crystal Structure of the NUAK1-MARK3 kinase domain chimera bound with small molecule inhibitor 2-amino-N-(5-((5-chloro-4-(((3R,3aR,6R,6aR)-6-methoxyhexahydrofuro[3,2-b]furan-3-yl)oxy)pyrimidin-2-yl)amino)-2-((2-(dimethylamino)ethyl)(methyl)amino)phenyl)acetamide ;

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