MolNFT v1 · #168473 · protein
Histone deacetylases complex with peptide macrocycles
6WHQ · Histone deacetylase 2: “Histone deacetylases complex with peptide macrocycles”. X-ray diffraction, 2 ligands (NA, ZN), 3 pockets (best druggability 0.72). MolNFT v1 #168473 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WHQ
- Type
- protein
- Length
- 1,126 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 2; U2M-asn-pro-glu-gln-dly-TRP-gly peptide macrocycle
- EC
- 3.5.1.98
- UniProt
- Q92769
- Ligands
- NA, ZN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 2 (EC 3.5.1.98) | protein | 374 | 40% helix, 12% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 366 | 40% helix, 12% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 365 | 40% helix, 12% strand | Q92769 |
| F, G | U2M-asn-pro-glu-gln-dly-TRP-gly peptide macrocycle | protein | 8 | 0% helix, 0% strand | — |
| H | U2M-asn-pro-glu-gln-dly-TRP-gly peptide macrocycle | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, F, B, G, C, H
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.72 | 0.79 | 69 | PG4, PGE |
| 2 | 643 | 0.68 | 0.77 | 61 | empty |
| 3 | 206 | 0.53 | 0.77 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–C · 704 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 592 Ų buried · 15 hydrogen bonds · protein-protein
- B–G · 454 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 420 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 416 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 2 d-amino (nonstandard, D-amino acid).
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 6WHQ · PDBe 6WHQ · UniProt Q92769
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