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9t9h

Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2n

Method: X-RAY DIFFRACTION D_max: 66.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t9h
deposition_date	2025-11-14
title	Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2n
keywords	Chromatin Remodeler, Chromodomain, Epigenetic Reader, Inhibitor, Prostate Cancer, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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	19.25 Å
rg_electron	18.57 Å
i0	15436700.00
molecular_weight	19790.0 kDa
excluded_volume	19130 Å³
envelope_volume	32198 Å³
shell_volume	15353 Å³
envelope_diameter	67.0 Å
shell_rg	23.57 Å
envelope_rg	18.88 Å
shape_rg	18.56 Å
total_rg	19.20 Å
total_atoms	1496
n_residues	174
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	66.3 Å
rg_real	19.27 Å
rg_real_error	0.51 Å
i0_real	1.5440e+07
i0_real_error	2.1880e+05
rg_reciprocal	19.27 Å
i0_reciprocal	15440000.0000
total_estimate	0.7092
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.0 Å
skewness	0.386
kurtosis	-0.185
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	1787000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 0.295; Positv: 1.000; Valcen: 0.938; Smooth: 0.951

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Chromodomain-helicase-DNA-binding protein 1
formula_weight	20483.8 kDa
ec_number	3.6.4.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1722

EFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	7-ethoxy-2-[4-[(4-methoxyphenyl)methylamino]piperidin-1-yl]-~{N}-[1-(phenylmethyl)piperidin-4-yl]quinolin-4-amine
formula_weight	579.8 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	212

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6. Citations (1)

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length_a	44.958 Å
length_b	46.241 Å
length_c	110.173 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 2 21
int_tables_number	18
crystal_system	—

resolution	1.450 Å
resolution_low	23.490 Å
r_factor	0.2009
r_work	0.2005
r_free	0.2080

fit	/app/data/saxs_computation/t9/9t9h/9t9h.fit
pddf	/app/data/pr_computation/t9/9t9h/9t9h.pr.out
profile	/app/data/saxs_computation/t9/9t9h/9t9h.dat