MolNFT v1 · #181388 · protein
Structure of human HDAC2 in complex with apicidin
7LTG · Histone deacetylase 2: “Structure of human HDAC2 in complex with apicidin”. X-ray diffraction, 3 ligands (YED, CA, ZN), 4 pockets (best druggability 0.73). MolNFT v1 #181388 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7LTG
- Type
- protein
- Length
- 1,099 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
- YED, CA, ZN
- Pockets
- 4 · 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 | 367 | 40% helix, 13% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 365 | 42% helix, 13% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 367 | 40% helix, 13% strand | Q92769 |
Ligands and binding sites
- YED · (3s,6s,9s,15ar)-9-[(2S)-butan-2-yl]-3-(6,6-dihydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl) methyl]octahydro-2H-pyrido[1,2-A][1,4,7, 10]tetraazacyclododecine-1,4,7,10(3H,12H)-tetrone · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 6 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.73 | 0.78 | 73 | PEG |
| 2 | 475 | 0.63 | 0.76 | 43 | empty |
| 3 | 231 | 0.56 | 0.78 | 21 | empty |
| 4 | 55 | 0.25 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 658 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 567 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 376 Ų buried · 6 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 7LTG · PDBe 7LTG · UniProt Q92769
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