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9t9e

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

Method: X-RAY DIFFRACTION D_max: 67.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t9e
deposition_date	2025-11-14
title	Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2b
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	19.18 Å
rg_electron	18.45 Å
i0	14839100.00
molecular_weight	19326.0 kDa
excluded_volume	18672 Å³
envelope_volume	31624 Å³
shell_volume	15155 Å³
envelope_diameter	67.3 Å
shell_rg	23.49 Å
envelope_rg	18.84 Å
shape_rg	18.42 Å
total_rg	19.14 Å
total_atoms	1462
n_residues	172
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	67.4 Å
rg_real	19.20 Å
rg_real_error	0.54 Å
i0_real	1.4840e+07
i0_real_error	1.9900e+05
rg_reciprocal	19.20 Å
i0_reciprocal	14840000.0000
total_estimate	0.8638
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.390
kurtosis	-0.166
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	1718000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.973

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	1617

EFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	~{N}2-[3-(dimethylamino)propyl]-7-ethoxy-~{N}4-[1-(phenylmethyl)piperidin-4-yl]quinoline-2,4-diamine
formula_weight	461.6 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	149

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6. Citations (1)

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length_a	44.730 Å
length_b	46.096 Å
length_c	110.012 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	1.700 Å
resolution_low	28.700 Å
r_factor	0.2037
r_work	0.2027
r_free	0.2208

fit	/app/data/saxs_computation/t9/9t9e/9t9e.fit
pddf	/app/data/pr_computation/t9/9t9e/9t9e.pr.out
profile	/app/data/saxs_computation/t9/9t9e/9t9e.dat

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

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