MolNFT v1 · #134255 · protein
Cocrystal structure of the human acyl protein thioesterase 2 with an isoform-selective inhibitor, ML349
5SYN · Acyl-protein thioesterase 2: “Cocrystal structure of the human acyl protein thioesterase 2 with an isoform-selective inhibitor, ML349”. X-ray diffraction, 1 ligand (71T), 12 pockets (best druggability 0.76). MolNFT v1 #134255 on…
- PDB
- 5SYN
- Type
- protein
- Length
- 889 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-protein thioesterase 2
- EC
- 3.1.2.-
- UniProt
- O95372
- Ligands
- 71T
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acyl-protein thioesterase 2 (EC 3.1.2.-) | protein | 223 | 37% helix, 23% strand | O95372 |
| C | Acyl-protein thioesterase 2 (EC 3.1.2.-) | protein | 221 | 34% helix, 23% strand | O95372 |
| D | Acyl-protein thioesterase 2 (EC 3.1.2.-) | protein | 222 | 36% helix, 22% strand | O95372 |
Ligands and binding sites
- 71T · 2-[4-(4-methoxyphenyl)piperazine-1-carbonyl]-5lambda~6~-thieno[3,2-c][1]benzothiopyran-5,5(4H)-dione · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.76 | 0.91 | 32 | empty |
| 2 | 522 | 0.69 | 0.79 | 64 | 71T |
| 3 | 226 | 0.67 | 0.84 | 33 | 71T |
| 4 | 241 | 0.66 | 0.83 | 36 | 71T |
| 5 | 212 | 0.65 | 0.83 | 37 | 71T |
Interfaces
4 interfaces between chains.
- A–B · 914 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 399 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 277 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 86 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5SYN · Cocrystal structure of the human acyl protein thioesterase 2 with an isoform-selective… · the same entry in another collection · chain A against A, TM-score 1.00
- O95372 · AlphaFold monomer V2.0 prediction for acyl-protein thioesterase 2 (O95372) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O95372
- Elsewhere: RCSB PDB 5SYN · PDBe 5SYN · UniProt O95372
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.