MolNFT v1 · #156858 · protein
Glutathione S-transferase omega 1 bound to covalent inhibitor 44
6MHD · Glutathione S-transferase omega-1: “Glutathione S-transferase omega 1 bound to covalent inhibitor 44”. X-ray diffraction, 2 ligands (JRD, ACN), 5 pockets (best druggability 0.78). MolNFT v1 #156858 on GenesisL1: 3D structure…
- PDB
- 6MHD
- Type
- protein
- Length
- 488 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase omega-1
- EC
- 2.5.1.18, 1.8.5.1, 1.20.4.2
- UniProt
- P78417
- Ligands
- JRD, ACN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione S-transferase omega-1 (EC 2.5.1.18, 1.8.5.1, 1.20.4.2) | protein | 244 | 49% helix, 9% strand | P78417 |
Ligands and binding sites
- JRD · N-[(3-methyl-1,2-oxazol-5-yl)methyl]-N-(4-phenyl-1,3-thiazol-2-yl)propanamide · ligand · 2 copies · chains A, B
- ACN · Acetone · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.78 | 0.80 | 93 | JRD, MES, ACN |
| 2 | 197 | 0.48 | 0.75 | 23 | empty |
| 3 | 171 | 0.44 | 0.74 | 23 | empty |
| 4 | 104 | 0.43 | 0.78 | 18 | empty |
| 5 | 106 | 0.42 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 976 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6MHD · Glutathione S-Transferase Omega 1 bound to covalent inhibitor 44 · the same entry in another collection · chain A against A, TM-score 1.00
- P78417 · AlphaFold monomer V2.0 prediction for glutathione S-transferase omega-1 (P78417) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P78417
- Elsewhere: RCSB PDB 6MHD · PDBe 6MHD · UniProt P78417
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