Research workbench
Structural basis for the binding of the anti-cancer compound 6-(7- nitro-2,1,3-benzoxadiazol-4-YLTHIO)HEXANOL (nbdhex) to human glutathione S-transferases
Analyse Structural basis for the binding of the anti-cancer compound 6-(7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IE3
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione S-transferase P
- EC
- 2.5.1.18
- UniProt
- P09211
- Ligands
- GSH, N11
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione S-transferase P (EC 2.5.1.18) | protein | 209 | 63% helix, 9% strand | P09211 |
| B | Glutathione S-transferase P (EC 2.5.1.18) | protein | 208 | 62% helix, 9% strand | P09211 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B
- N11 · 6-[(7-nitro-2,1,3-benzoxadiazol-4-yl)sulfanyl]hexan-1-ol · 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 | 663 | 0.72 | 0.79 | 81 | GSH, N11 |
| 2 | 97 | 0.39 | 0.76 | 18 | empty |
| 3 | 57 | 0.36 | 0.79 | 15 | empty |
| 4 | 57 | 0.32 | 0.76 | 13 | empty |
| 5 | 71 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1306 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3IE3 · Structural basis for the binding of the anti-cancer compound… · the same entry in another collection · 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 P09211
- Elsewhere: RCSB PDB 3IE3 · PDBe 3IE3 · UniProt P09211
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.