MolNFT v1 · #179629 · protein
Structure of human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16)
7KBH · Histone deacetylase 2: “Structure of human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16)”. X-ray diffraction, 3 ligands (WB4, CA, ZN), 5 pockets (best druggability 0.73). MolNFT v1 #179629 on GenesisL1: 3D…
- PDB
- 7KBH
- Type
- protein
- Length
- 1,102 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
- WB4, CA, ZN
- Pockets
- 5 · best druggability 0.73
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 | 369 | 39% helix, 13% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 366 | 42% helix, 12% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 367 | 40% helix, 13% strand | Q92769 |
Ligands and binding sites
- WB4 · N-{(1S)-5-{[2-(methylsulfanyl)benzene-1-carbonyl]amino}-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide · 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 · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.73 | 0.78 | 68 | empty |
| 2 | 718 | 0.70 | 0.77 | 66 | empty |
| 3 | 87 | 0.66 | 0.91 | 22 | WB4 |
| 4 | 87 | 0.66 | 0.91 | 23 | WB4 |
| 5 | 92 | 0.65 | 0.91 | 23 | ZN, WB4 |
Interfaces
3 interfaces between chains.
- A–B · 628 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7KBH · Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16) · the same entry in another collection · chain A against A, TM-score 1.00
- Q92769 · AlphaFold monomer V2.0 prediction for histone deacetylase 2 (Q92769) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 7KBH · PDBe 7KBH · UniProt Q92769
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