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9szj

Crystal structure of Y1230H c-MET bound by capmatinib.

Method: X-RAY DIFFRACTION D_max: 62.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9szj
deposition_date	2025-10-14
title	Crystal structure of Y1230H c-MET bound by capmatinib.
keywords	Kinase, c-met, drug discovery, cancer, NSCLC, 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	19.19 Å
rg_electron	18.40 Å
i0	27300900.00
molecular_weight	27355.0 kDa
excluded_volume	26789 Å³
envelope_volume	42723 Å³
shell_volume	19318 Å³
envelope_diameter	63.4 Å
shell_rg	24.87 Å
envelope_rg	18.76 Å
shape_rg	18.39 Å
total_rg	19.13 Å
total_atoms	2075
n_residues	262
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	62.2 Å
rg_real	19.11 Å
rg_real_error	0.27 Å
i0_real	2.7300e+07
i0_real_error	3.3040e+05
rg_reciprocal	19.13 Å
i0_reciprocal	27300000.0000
total_estimate	0.8894
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.3 Å
skewness	0.271
kurtosis	-0.329
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	6459000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Hepatocyte growth factor receptor
formula_weight	34817.3 kDa
ec_number	2.7.10.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2103

GDSDISSPLLQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMHDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	Capmatinib
formula_weight	412.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	20

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6. Citations (1)

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length_a	42.264 Å
length_b	43.386 Å
length_c	158.328 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.289 Å
resolution_low	79.160 Å
r_factor	0.2339
r_work	0.2300
r_free	0.3037

fit	/app/data/saxs_computation/sz/9szj/9szj.fit
pddf	/app/data/pr_computation/sz/9szj/9szj.pr.out
profile	/app/data/saxs_computation/sz/9szj/9szj.dat

Crystal structure of Y1230H c-MET bound by capmatinib.

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