Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with compound LC-F2-01

Method: X-RAY DIFFRACTION D_max: 88.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u3n
deposition_date	2025-03-18
last_revision	2025-04-23
title	Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with compound LC-F2-01
keywords	FGFR2, 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	28.19 Å
rg_electron	27.50 Å
i0	124446000.00
molecular_weight	58898.0 kDa
excluded_volume	56998 Å³
envelope_volume	103620 Å³
shell_volume	31343 Å³
envelope_diameter	92.4 Å
shell_rg	34.91 Å
envelope_rg	27.22 Å
shape_rg	27.48 Å
total_rg	28.10 Å
total_atoms	4440
n_residues	548
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	88.3 Å
rg_real	28.12 Å
rg_real_error	0.56 Å
i0_real	1.2440e+08
i0_real_error	1.9210e+06
rg_reciprocal	28.14 Å
i0_reciprocal	124400000.0000
total_estimate	0.9067
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	31.6 Å
skewness	0.214
kurtosis	-0.576
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	42250000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.939

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	63.069 Å
length_b	88.713 Å
length_c	127.420 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	3.250 Å
resolution_low	47.670 Å
r_factor	—
r_work	0.2793
r_free	0.3419

description	Fibroblast growth factor receptor 2
formula_weight	35669.1 kDa
ec_number	2.7.10.1
mutation	V564F
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	4440

Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with compound LC-F2-01

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

description	~{N}-[4-[4-azanyl-7-methyl-5-[2-(3-methylimidazo[4,5-b]pyridin-6-yl)ethynyl]pyrrolo[2,3-d]pyrimidin-6-yl]phenyl]prop-2-enamide
formula_weight	448.5 kDa
src_method	syn
entity_count	2

fit	/app/data/saxs_computation/u3/9u3n/9u3n.fit
pddf	/app/data/pr_computation/u3/9u3n/9u3n.pr.out
profile	/app/data/saxs_computation/u3/9u3n/9u3n.dat