SAXSdb — 9t9e

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromodomain-helicase-DNA-binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 270–443	Not recorded	A1JUQ ~{N}2-[3-(dimethylamino)propyl]-7-ethoxy-~{N}4-[1-(phenylmethyl)piperidin-4-yl]quinoline-2,4-diamine × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；281 K；12 % (w/v) PEG 3350, 0.2 M L-Proline, 0.1 M HEPES, pH 7.5. The ligand (final conc. of 20 mM, 10% (v/v) DMSO) has been soaked in this condition for 24 h.	Resolution 1.70 Å R-free 0.221

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9T9E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2B2T Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and phosphothreonine 3 Deposited 2005-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 268–443（176 aa） Fragment：residues 268-443 Chain B 268–443（176 aa） Fragment：residues 268-443 Chain C 268–373（106 aa） Fragment：residues 268-373	Mutation：C436M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C436M Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00	Resolution 2.45 Å R-free 0.266
2B2U Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and dimethylarginine 2 Deposited 2005-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 268–443（176 aa） Fragment：residues 268-443 Chain B 268–443（176 aa） Fragment：residues 268-443 Chain C 268–373（106 aa） Fragment：residues 268-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00	Resolution 2.95 Å R-free 0.290
2B2V Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4 Deposited 2005-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 268–443（176 aa） Fragment：residues 268-443 Chain B 268–443（176 aa） Fragment：residues 268-443 Chain C 268–373（106 aa） Fragment：residues 268-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00	Resolution 2.65 Å R-free 0.266
2B2W Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 Deposited 2005-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 268–443（176 aa） Fragment：residues 268-443 Chain B 268–443（176 aa） Fragment：residues 268-443 Chain C 268–373（106 aa） Fragment：residues 268-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00	Resolution 2.40 Å R-free 0.273
2B2Y Tandem chromodomains of human CHD1 Deposited 2005-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 268–443（176 aa） Fragment：residues 268-443 Chain B 268–443（176 aa） Fragment：residues 268-443 Chain C 268–373（106 aa） Fragment：residues 268-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES, 10mM BTP, pH 8.0, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00	Resolution 2.35 Å R-free 0.264
2N39 NMR solution structure of a C-terminal domain of the chromodomain helicase DNA-binding protein 1 Deposited 2015-05-26	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1409–1511（103 aa） Fragment：C-terminal domain (UNP residues 1409-1511)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition 440 uM [U-98% 13C; U-98% 15N] CHD1-C, 20 mM sodium phosphate, 10 mM NaCl, 1 mM DTT, 0.003 w/v sodium azide, 0.2 mM 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4B4C Crystal structure of the DNA-binding domain of human CHD1. Deposited 2012-07-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1119–1327（209 aa） Fragment：DNA-BINDING DOMAIN, RESIDUES 1119-1327	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；2M AMMONIUM SULFATE, 0.1M CITRATE PH 3.5	Resolution 1.62 Å R-free 0.226
4NW2 Tandem chromodomains of human CHD1 in complex with Influenza virus NS1 C-terminal tail trimethylated at K229 Deposited 2013-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 268–443（176 aa） Fragment：UNP residues 268-443	Not recorded	UNX UNKNOWN LIGAND × 18 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；10% PEG8000, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K	Resolution 1.90 Å R-free 0.242
4NW2 Tandem chromodomains of human CHD1 in complex with Influenza virus NS1 C-terminal tail trimethylated at K229 Deposited 2013-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 268–443（176 aa） Fragment：UNP residues 268-443	Not recorded	UNX UNKNOWN LIGAND × 13 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；10% PEG8000, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K	Resolution 1.90 Å R-free 0.242
4O42 Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229 Deposited 2013-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 268–443（176 aa） Fragment：UNP residues 268-443	Not recorded	UNX UNKNOWN LIGAND × 11 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；291 K；15% PEG3350, 0.1 succinic acid, pH 7, temperature 291K	Resolution 1.87 Å R-free 0.221
5AFW Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation Deposited 2015-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 270–443（174 aa） Fragment：RESIDUES 270-443	Not recorded	EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M HEPES PH 7.5, 0.2 M L-PROLINE, 10% (W/V) PEG3350	Resolution 1.60 Å R-free 0.227
8UMG Chromodomains of human CHD1 complexed with UNC10142 Deposited 2023-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 268–445（178 aa） Chain B 268–445（178 aa） Chain C 268–445（178 aa）	Mutation：+KK Mutation：+KK Mutation：+KK	X31 1-{4-[{2-(azonan-1-yl)-6-methoxy-7-[3-(piperidin-1-yl)propoxy]quinazolin-4-yl}(methyl)amino]piperidin-1-yl}ethan-1-one × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG3350, sodium chloride, HEPES	Resolution 3.10 Å R-free 0.320
9EAR CHD1-nucleosome complex (closed state) Deposited 2024-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric	Chain W 2–1327（1326 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9NH8 CHD1-nucleosome complex (anchored state) Deposited 2025-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric	Chain W 2–1327（1326 aa）	Not recorded	ARG ARGININE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9T9F Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2l Deposited 2025-11-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 270–443（174 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 A1JUR 2-[4-(dimethylamino)piperidin-1-yl]-7-ethoxy-~{N}-[1-(phenylmethyl)piperidin-4-yl]quinolin-4-amine × 1 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；12 % (w/v) PEG 3350, 0.2 M L-Proline, 0.1 M HEPES, pH 7.5. The ligand (final conc. of 10 mM, 10% (v/v) DMSO) has been soaked in this condition for 24 h.	Resolution 1.35 Å R-free 0.208
9T9G Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinazoline-based inhibitor 1q Deposited 2025-11-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 270–443（174 aa）	Not recorded	A1JUO 2-[4-(dimethylamino)piperidin-1-yl]-7-ethoxy-~{N}-[1-(phenylmethyl)piperidin-4-yl]quinazolin-4-amine × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；12 % (w/v) PEG 3350, 0.2 M L-Proline, 0.1 M HEPES, pH 7.5. The ligand (final conc. of 20 mM, 10 % (v/v) DMSO) has been soaked in this condition for 24 h.	Resolution 1.70 Å R-free 0.212
9T9H Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2n Deposited 2025-11-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 270–443（174 aa）	Not recorded	A1JUP 7-ethoxy-2-[4-[(4-methoxyphenyl)methylamino]piperidin-1-yl]-~{N}-[1-(phenylmethyl)piperidin-4-yl]quinolin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；12 % (w/v) PEG 3350, 0.2 M L-Proline, 0.1 M HEPES, pH 7.5. The ligand (final conc. of 10 mM, 10% (v/v) DMSO) has been soaked in this condition for 24 h.	Resolution 1.45 Å R-free 0.208
9T9I Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2s Deposited 2025-11-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 270–443（174 aa）	Not recorded	A1JUS 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 × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；12 % (w/v) PEG 3350, 0.2 M L-Proline, 0.1 M HEPES, pH 7.5. The ligand (final conc. of 10 mM, 10% (v/v) DMSO) has been soaked in this condition for 24 h.	Resolution 1.55 Å R-free 0.217

17 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–174； UniProt 270–443

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9t9e
Deposition date deposition_date	2025-11-14
Structure title title	Crystal structure of human CHD1 tandem chromodomain in complex with the ethoxyquinoline-based inhibitor 2b
Keywords keywords	Chromatin Remodeler, Chromodomain, Epigenetic Reader, Inhibitor, Prostate Cancer, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.18 Å
Radius of gyration Rg (electron density) rg_electron	18.45 Å
Forward intensity I(0) i0	14839100.00
Molecular weight molecular_weight	19326.0 kDa
Excluded volume excluded_volume	18672 Å³
Envelope volume envelope_volume	31624 Å³
Hydration-shell volume shell_volume	15155 Å³
Envelope diameter envelope_diameter	67.3 Å
Shell Rg shell_rg	23.49 Å
Envelope Rg envelope_rg	18.84 Å
Shape Rg shape_rg	18.42 Å
Total Rg total_rg	19.14 Å
Total atoms total_atoms	1462
Residues n_residues	172
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	67.4 Å
Rg (real space) rg_real	19.20 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	1.4840e+07
I(0) uncertainty (real space) i0_real_error	1.9900e+05
Rg (reciprocal space) rg_reciprocal	19.20 Å
I(0) (reciprocal space) i0_reciprocal	14840000.0000
Solution quality estimate total_estimate	0.8638
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.390
Kurtosis Kurtosis kurtosis	-0.166
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1718000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Chromodomain-helicase-DNA-binding protein 1
Molecular weight formula_weight	20483.8 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1617

EFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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8. Citations (1)

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Unit-cell length a length_a	44.730 Å
Unit-cell length b length_b	46.096 Å
Unit-cell length c length_c	110.012 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	28.700 Å
R factor r_factor	0.2037
R_work r_work	0.2027
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromodomain-helicase-DNA-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction