SAXSdb — 4cby

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

HISTONE DEACETYLASE 4

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZINC ION × 2 SODIUM ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZINC ION × 2 SODIUM ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZINC ION × 2 SODIUM ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZINC ION × 2 SODIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDAC4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–389； UniProt 648–1033 Author chain B； PDBConstruct 4–389； UniProt 648–1033 Author chain C； PDBConstruct 4–389； UniProt 648–1033 Author chain D； PDBConstruct 4–389； UniProt 648–1033

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	4cby
Deposition date deposition_date	2013-10-17
Structure title title	Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease
Keywords keywords	;HYDROLASE, NEURODEGENERATION, AMYOTROPHIC LATERAL SCLEROSIS, MUSCLE ATROPHY, CLASS IIA HISTONE DEACETYLASE INHIBITORS, SAR, HYDROXAMIC ACID, CYCLOPROPANATION ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4cby__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4cby__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4cby__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.86 Å
Rg (electron density)	19.77 Å
Total Rg	20.76 Å
Atom count	2851
Residues	380
Excluded volume	50680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4cby__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4cby__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4cby__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4cby__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	HISTONE DEACETYLASE 4
Molecular weight formula_weight	42755.6 kDa
EC 编号 ec_number	3.5.1.98
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11435

MGSTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPANRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRHHHHHH

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	(1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide
Molecular weight formula_weight	320.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d4cbya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.2 — Histone deacetylase, HDAC

Domain ID domain_id	d4cbyb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.2 — Histone deacetylase, HDAC

Domain ID domain_id	d4cbyc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.2 — Histone deacetylase, HDAC

Domain ID domain_id	d4cbyd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.2 — Histone deacetylase, HDAC

Domain ID domain_id	d4cbyd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	4cbyA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	4cbyB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	4cbyC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	4cbyD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

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Unit-cell length a length_a	54.151 Å
Unit-cell length b length_b	161.816 Å
Unit-cell length c length_c	83.732 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.720 Å
Low-resolution limit resolution_low	83.100 Å
R factor r_factor	0.2110
R_work r_work	0.2091
R_free r_free	0.2459

Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease

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

HISTONE DEACETYLASE 4

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4cby__assembly_1__model_1

4cby__assembly_1__model_1 | I(q)

4cby__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease

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

HISTONE DEACETYLASE 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4cby__assembly_1__model_1

4cby__assembly_1__model_1 | I(q)

4cby__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)