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9qxn

Crystal Structure of wild-type EGFR in complex with the reversible inhibitor Sevabertinib (BAY 2927088)

Method: X-RAY DIFFRACTION D_max: 67.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qxn
deposition_date	2025-04-16
title	Crystal Structure of wild-type EGFR in complex with the reversible inhibitor Sevabertinib (BAY 2927088)
keywords	KINASE, INHIBITOR, COMPLEX, REVERSIBLE, CANCER, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, 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	21.24 Å
rg_electron	20.30 Å
i0	45522200.00
molecular_weight	35199.0 kDa
excluded_volume	34176 Å³
envelope_volume	56961 Å³
shell_volume	22933 Å³
envelope_diameter	70.6 Å
shell_rg	27.36 Å
envelope_rg	20.77 Å
shape_rg	20.27 Å
total_rg	21.05 Å
total_atoms	2655
n_residues	324
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	67.6 Å
rg_real	21.14 Å
rg_real_error	0.32 Å
i0_real	4.5520e+07
i0_real_error	5.3360e+05
rg_reciprocal	21.16 Å
i0_reciprocal	45520000.0000
total_estimate	0.8987
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.6 Å
skewness	0.220
kurtosis	-0.464
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	14270000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Epidermal growth factor receptor
formula_weight	39570.7 kDa
ec_number	2.7.10.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AAA
atom_count	3162

MSHHHHHAMTENLYFQGAMGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	SUCCINIC ACID
formula_weight	118.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	;3-[(3-chloranyl-2-methoxy-phenyl)amino]-2-[3-[[(2~{S})-1,4-dioxan-2-yl]methoxy]pyridin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-one ;
formula_weight	484.9 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	450

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6. Citations (1)

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length_a	147.430 Å
length_b	147.430 Å
length_c	147.430 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	I 2 3
int_tables_number	197
crystal_system	—

resolution	2.142 Å
resolution_low	28.930 Å
r_factor	—
r_work	0.1561
r_free	0.2102

fit	/app/data/saxs_computation/qx/9qxn/9qxn.fit
pddf	/app/data/pr_computation/qx/9qxn/9qxn.pr.out
profile	/app/data/saxs_computation/qx/9qxn/9qxn.dat