Research workbench
H-pgds complexed with inhibitor 1Y
Analyse H-pgds complexed with inhibitor 1Y in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W8H
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hematopoietic prostaglandin D synthase
- EC
- 5.3.99.2, 2.5.1.18
- UniProt
- O60760
- Ligands
- GSH, TJG
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 198 | 57% helix, 10% strand | O60760 |
| C | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 199 | 58% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, C
- TJG · 7-cyclopropyl-N-[trans-4-(2-hydroxypropan-2-yl) cyclohexyl]-1,8-naphthyridine-3-carboxamide · ligand · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.79 | 0.80 | 83 | GSH, TJG |
| 2 | 87 | 0.48 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–C · 1408 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 O60760
- Elsewhere: RCSB PDB 6W8H · PDBe 6W8H · UniProt O60760
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.