MolNFT v1 · #156856 · protein

Glutathione S-transferase omega 1 bound to covalent inhibitor 18

6MHB · Glutathione S-transferase omega-1: “Glutathione S-transferase omega 1 bound to covalent inhibitor 18”. X-ray diffraction, 1 ligand (JR7), 20 pockets (best druggability 0.81). MolNFT v1 #156856 on GenesisL1: 3D structure, binding…

PDB: 6MHB
Type: protein
Length: 1,388 residues
Chains: 6
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: JR7
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 53% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Glutathione S-transferase omega-1 (EC 2.5.1.18, 1.8.5.1, 1.20.4.2)	protein	233	54% helix, 9% strand	P78417
C	Glutathione S-transferase omega-1 (EC 2.5.1.18, 1.8.5.1, 1.20.4.2)	protein	233	54% helix, 9% strand	P78417
E	Glutathione S-transferase omega-1 (EC 2.5.1.18, 1.8.5.1, 1.20.4.2)	protein	224	53% helix, 8% strand	P78417
F	Glutathione S-transferase omega-1 (EC 2.5.1.18, 1.8.5.1, 1.20.4.2)	protein	232	53% helix, 9% strand	P78417

Ligands and binding sites

JR7 · N-[4-(4-chlorophenyl)-1,3-thiazol-2-yl]propanamide · ligand · 6 copies · chains A, B, C, D, E, F
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, C, D, E, B, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	931	0.81	0.82	120	JR7, MES
2	787	0.80	0.83	76	JR7, MES
3	531	0.74	0.81	50	MES
4	158	0.67	0.87	34	empty
5	300	0.63	0.80	44	empty

Interfaces

9 interfaces between chains.

A–C · 989 Å² buried · 2 hydrogen bonds · protein-protein
D–E · 984 Å² buried · 3 hydrogen bonds · protein-protein
B–F · 977 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 199 Å² buried · 1 hydrogen bond · protein-protein
A–D · 183 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

6MHB · Glutathione S-Transferase Omega 1 bound to covalent inhibitor 18 · the same entry in another collection · chain F against F, 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 F 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 P78417
Elsewhere: RCSB PDB 6MHB · PDBe 6MHB · UniProt P78417

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.