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4cbt

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

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HISTONE DEACETYLASE 4

HOMO SAPIENS

UniProt P56524

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-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZINC ION × 2 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 (1R,2R,3R)-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZINC ION × 2 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 (1R,2R,3R)-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide × 1 ZINC ION × 2 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2vqj 2vqm 2vqo 2vqo 2vqq 2vqq 2vqv 2vqv 2vqw 4cbt 4cbt 4cbt

21 assemblies; showing the first 12

Homodimer

None

Homotetramer
2h8n 2o94

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
3uxg 3uxg 3uzd 3uzd 3uzd 3v31 5zoo 5zop 7xuz

9 assemblies

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

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_id4cbt
Deposition date deposition_date2013-10-16
Structure title titleDesign, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease
Keywords keywords;HYDROLASE, NEURODEGENERATION, HUNTINGTONS DISEASE, AMYOTROPHIC LATERAL SCLEROSIS, MUSCLE ATROPHY, CLASS IIA HISTONE DEACETYLASE INHIBITORS, SAR, HYDROXAMIC ACID, CYCLOPROPANATION ;; HYDROLASE
Experimental Method methodX-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.

4cbt__assembly_1__model_1

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

Download this curve (.dat)

4cbt__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4cbt__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）20.04 Å
Rg (electron density)18.83 Å
Total Rg19.86 Å
Atom count2666
Residues349
Excluded volume47102 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4cbt__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4cbt__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4cbt__assembly_3__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 (4)

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4cbta1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.2 — Histone deacetylase, HDAC
Domain ID domain_idd4cbta2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4cbtb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.2 — Histone deacetylase, HDAC
Domain ID domain_idd4cbtc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.2 — Histone deacetylase, HDAC
Domain ID domain_idd4cbtc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4cbtc3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id4cbtA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily20 — Histone deacetylase domain
Domain ID domain_id4cbtB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily20 — Histone deacetylase domain
Domain ID domain_id4cbtC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily20 — Histone deacetylase domain
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7. Citations (1)