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9t2v

Crystal structure of wild-type c-MET bound by cabozantinib.

Method: X-RAY DIFFRACTION D_max: 65.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t2v
deposition_date	2025-10-23
title	Crystal structure of wild-type c-MET bound by cabozantinib.
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	20.28 Å
rg_electron	19.51 Å
i0	32328900.00
molecular_weight	29942.0 kDa
excluded_volume	29295 Å³
envelope_volume	47023 Å³
shell_volume	20173 Å³
envelope_diameter	66.9 Å
shell_rg	25.83 Å
envelope_rg	19.83 Å
shape_rg	19.51 Å
total_rg	20.16 Å
total_atoms	2272
n_residues	290
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	65.9 Å
rg_real	20.23 Å
rg_real_error	0.33 Å
i0_real	3.2330e+07
i0_real_error	4.2200e+05
rg_reciprocal	20.24 Å
i0_reciprocal	32330000.0000
total_estimate	0.7059
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.5 Å
skewness	0.305
kurtosis	-0.372
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	7605000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 0.193; 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	33471.9 kDa
ec_number	2.7.10.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2467

GHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	Cabozantinib
formula_weight	501.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	192

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6. Citations (1)

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length_a	42.554 Å
length_b	80.379 Å
length_c	91.305 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	1.665 Å
resolution_low	60.330 Å
r_factor	—
r_work	0.1940
r_free	0.2260

fit	/app/data/saxs_computation/t2/9t2v/9t2v.fit
pddf	/app/data/pr_computation/t2/9t2v/9t2v.pr.out
profile	/app/data/saxs_computation/t2/9t2v/9t2v.dat

Crystal structure of wild-type c-MET bound by cabozantinib.

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