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9rda

Cocrystal structure of Zilurgisertib bound to the ALK2-FKBP12 complex

Method: X-RAY DIFFRACTION D_max: 88.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rda
deposition_date	2025-06-02
title	Cocrystal structure of Zilurgisertib bound to the ALK2-FKBP12 complex
keywords	kinase, 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	25.04 Å
rg_electron	24.48 Å
i0	76142800.00
molecular_weight	45611.0 kDa
excluded_volume	44053 Å³
envelope_volume	73197 Å³
shell_volume	25917 Å³
envelope_diameter	92.9 Å
shell_rg	30.80 Å
envelope_rg	24.61 Å
shape_rg	24.44 Å
total_rg	25.06 Å
total_atoms	3451
n_residues	427
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	88.2 Å
rg_real	25.17 Å
rg_real_error	0.64 Å
i0_real	7.6140e+07
i0_real_error	1.2040e+06
rg_reciprocal	25.13 Å
i0_reciprocal	76140000.0000
total_estimate	0.6303
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	26.6 Å
skewness	0.543
kurtosis	-0.151
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	15340000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.680; Stabil: 1.000; Sysdev: 0.120; Positv: 1.000; Valcen: 0.798; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Activin receptor type-1
formula_weight	37370.7 kDa
ec_number	2.7.11.30
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3875

SSMTTNVGDSTLADLLDHSCTSGSGSGLPFLVQRTVARQITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Peptidyl-prolyl cis-trans isomerase FKBP1A
formula_weight	11990.7 kDa
ec_number	5.2.1.8
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GPGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	Zilurgisertib
formula_weight	504.7 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	14

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	399

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6. Citations (1)

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length_a	43.620 Å
length_b	108.040 Å
length_c	115.200 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	1.748 Å
resolution_low	78.810 Å
r_factor	0.1954
r_work	0.1940
r_free	0.2236

fit	/app/data/saxs_computation/rd/9rda/9rda.fit
pddf	/app/data/pr_computation/rd/9rda/9rda.pr.out
profile	/app/data/saxs_computation/rd/9rda/9rda.dat

Cocrystal structure of Zilurgisertib bound to the ALK2-FKBP12 complex

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)