Research workbench
Crystal structure of a hdac-like protein with 9,9,9-trifluoro-8-oxo-N- phenylnonan amide bound
Analyse Crystal structure of a hdac-like protein with 9,9,9-trifluoro-8-oxo-N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GH6
- Type
- protein
- Length
- 1,468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase-like amidohydrolase
- EC
- 3.5.1.-
- UniProt
- Q70I53
- Ligands
- CF3, K, ZN
- Pockets
- 11 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Histone deacetylase-like amidohydrolase (EC 3.5.1.-) | protein | 367 | 39% helix, 14% strand | Q70I53 |
Ligands and binding sites
- CF3 · 9,9,9-trifluoro-8-oxo-N-phenylnonanamide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.90 | 0.93 | 108 | empty |
| 2 | 582 | 0.82 | 0.88 | 92 | empty |
| 3 | 707 | 0.82 | 0.86 | 92 | empty |
| 4 | 141 | 0.68 | 0.88 | 40 | CF3 |
| 5 | 458 | 0.63 | 0.76 | 45 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1723 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1712 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 954 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 940 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 393 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2GH6 · Crystal structure of a HDAC-like protein with 9,9,9-trifluoro-8-oxo-N-phenylnonan amide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q70I53 · AlphaFold monomer V2.0 prediction for histone deacetylase-like amidohydrolase (Q70I53) · a predicted model of the same protein · chain A 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 Q70I53
- Elsewhere: RCSB PDB 2GH6 · PDBe 2GH6 · UniProt Q70I53
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