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Structure of human HDAC2 in complex with saha (vorinostat)
Analyse Structure of human HDAC2 in complex with saha (vorinostat) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LXZ
- Type
- protein
- Length
- 1,103 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 2
- EC
- 3.5.1.98
- UniProt
- Q92769
- Ligands
- SHH, ZN, CA, NA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 2 (EC 3.5.1.98) | protein | 368 | 40% helix, 13% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 367 | 40% helix, 13% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 368 | 40% helix, 13% strand | Q92769 |
Ligands and binding sites
- SHH · Octanedioic acid hydroxyamide phenylamide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 8 copies · chains A, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.72 | 0.78 | 64 | PG4 |
| 2 | 590 | 0.66 | 0.76 | 47 | empty |
| 3 | 264 | 0.58 | 0.78 | 25 | empty |
| 4 | 63 | 0.29 | 0.74 | 12 | empty |
| 5 | 61 | 0.28 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 664 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 559 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 375 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q92769
- Elsewhere: RCSB PDB 4LXZ · PDBe 4LXZ · UniProt Q92769
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