MolNFT v1 · #134254 · protein
Cocrystal structure of the human acyl protein thioesterase 1 with an isoform-selective inhibitor, ML348
5SYM · Acyl-protein thioesterase 1: “Cocrystal structure of the human acyl protein thioesterase 1 with an isoform-selective inhibitor, ML348”. X-ray diffraction, 2 ligands (71Q, CL), 3 pockets (best druggability 0.84). MolNFT v1 #134254 on…
- PDB
- 5SYM
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-protein thioesterase 1
- EC
- 3.1.2.-
- UniProt
- O75608
- Ligands
- 71Q, CL
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acyl-protein thioesterase 1 (EC 3.1.2.-) | protein | 223 | 35% helix, 21% strand | O75608 |
Ligands and binding sites
- 71Q · N-[2-chloro-5-(trifluoromethyl)phenyl]-2-[4-(furan-2-carbonyl)piperazin-1-yl]acetamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.84 | 0.90 | 70 | 71Q, CL |
| 2 | 93 | 0.37 | 0.75 | 21 | empty |
| 3 | 72 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5SYM · Cocrystal structure of the human acyl protein thioesterase 1 with an isoform-selective… · the same entry in another collection · chain A against A, TM-score 1.00
- O75608 · AlphaFold monomer V2.0 prediction for acyl-protein thioesterase 1 (O75608) · a predicted model of the same protein · chain A 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 O75608
- Elsewhere: RCSB PDB 5SYM · PDBe 5SYM · UniProt O75608
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