MolNFT v1 · #99253 · protein
Structure of human HDAC2 in complex with inhibitor 4-(acetylamino)-N- [2-amino-5-(thiophen-2-YL)PHENYL]BENZAMIDE
4LY1 · Histone deacetylase 2: “Structure of human HDAC2 in complex with inhibitor 4-(acetylamino)-N…”. X-ray diffraction, 4 ligands (20Y, ZN, CA), 7 pockets (best druggability 0.73). MolNFT v1 #99253 on GenesisL1: 3D structure, binding…
- PDB
- 4LY1
- Type
- protein
- Length
- 1,101 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
- 20Y, ZN, CA, NA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 2 (EC 3.5.1.98) | protein | 368 | 41% 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 | 366 | 42% helix, 13% strand | Q92769 |
Ligands and binding sites
- 20Y · 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide · 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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.73 | 0.78 | 82 | PG4 |
| 2 | 568 | 0.67 | 0.77 | 56 | empty |
| 3 | 102 | 0.64 | 0.89 | 33 | 20Y |
| 4 | 89 | 0.64 | 0.90 | 27 | 20Y |
| 5 | 76 | 0.63 | 0.91 | 27 | 20Y |
Interfaces
3 interfaces between chains.
- A–C · 655 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 560 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 377 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 4LY1 · PDBe 4LY1 · UniProt Q92769
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