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9t9i

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

Method: X-RAY DIFFRACTION D_max: 66.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t9i
deposition_date	2025-11-14
title	Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2s
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	19.36 Å
rg_electron	18.64 Å
i0	15638000.00
molecular_weight	19876.0 kDa
excluded_volume	19208 Å³
envelope_volume	32470 Å³
shell_volume	15443 Å³
envelope_diameter	67.1 Å
shell_rg	23.72 Å
envelope_rg	18.88 Å
shape_rg	18.63 Å
total_rg	19.30 Å
total_atoms	1505
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	66.7 Å
rg_real	19.38 Å
rg_real_error	0.48 Å
i0_real	1.5640e+07
i0_real_error	2.0560e+05
rg_reciprocal	19.38 Å
i0_reciprocal	15640000.0000
total_estimate	0.8723
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.5 Å
skewness	0.389
kurtosis	-0.187
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	1807000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.971

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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	1720

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-[[1-(2-methoxyethyl)-1,2,3-triazol-4-yl]methoxy]phenyl]methylamino]piperidin-1-yl]-~{N}-[1-(phenylmethyl)piperidin-4-yl]quinolin-4-amine ;
formula_weight	704.9 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	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	195

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6. Citations (1)

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length_a	44.947 Å
length_b	46.160 Å
length_c	110.039 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	1.550 Å
resolution_low	46.160 Å
r_factor	0.1887
r_work	0.1870
r_free	0.2174

fit	/app/data/saxs_computation/t9/9t9i/9t9i.fit
pddf	/app/data/pr_computation/t9/9t9i/9t9i.pr.out
profile	/app/data/saxs_computation/t9/9t9i/9t9i.dat

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

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