← Back to search

9t9f

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

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

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9t9f
deposition_date	2025-11-14
title	Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2l
keywords	Chromatin Remodeler, Chromodomain, Epigenetic Reader, Inhibitor, Prostate Cancer, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	19.38 Å
rg_electron	18.65 Å
i0	15622400.00
molecular_weight	19814.0 kDa
excluded_volume	19124 Å³
envelope_volume	32603 Å³
shell_volume	15476 Å³
envelope_diameter	67.2 Å
shell_rg	23.75 Å
envelope_rg	18.99 Å
shape_rg	18.62 Å
total_rg	19.33 Å
total_atoms	1497
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

▼

3. P(r) Analysis (GNOM)

dmax	65.9 Å
rg_real	19.40 Å
rg_real_error	0.49 Å
i0_real	1.5620e+07
i0_real_error	2.0740e+05
rg_reciprocal	19.40 Å
i0_reciprocal	15620000.0000
total_estimate	0.8005
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.2 Å
skewness	0.405
kurtosis	-0.149
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	1891000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

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	1792

EFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	2-[4-(dimethylamino)piperidin-1-yl]-7-ethoxy-~{N}-[1-(phenylmethyl)piperidin-4-yl]quinolin-4-amine
formula_weight	487.7 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	246

▶

6. Citations (1)

▶

length_a	45.151 Å
length_b	46.221 Å
length_c	110.028 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	1.350 Å
resolution_low	20.890 Å
r_factor	0.1858
r_work	0.1846
r_free	0.2078

fit	/app/data/saxs_computation/t9/9t9f/9t9f.fit
pddf	/app/data/pr_computation/t9/9t9f/9t9f.pr.out
profile	/app/data/saxs_computation/t9/9t9f/9t9f.dat