Research workbench
Crystal structure of hh-pgds with water displacing inhibitor
Analyse Crystal structure of hh-pgds with water displacing inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EE0
- Type
- protein
- Length
- 389 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
- 0O4, GSF, MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 194 | 54% helix, 10% strand | O60760 |
| B | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 195 | 56% helix, 9% strand | O60760 |
Ligands and binding sites
- 0O4 · 4-(isoquinolin-1-yl)-N-[2-(morpholin-4-yl)ethyl]benzamide · ligand · 2 copies · chains A, B
- GSF · L-gamma-glutamyl-3-sulfino-L-alanylglycine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.78 | 0.80 | 92 | MG, 0O4, GSF |
| 2 | 80 | 0.53 | 0.85 | 21 | empty |
| 3 | 51 | 0.25 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4EE0 · Crystal structure of hH-PGDS with water displacing inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- O60760 · AlphaFold monomer V2.0 prediction for hematopoietic prostaglandin D synthase (O60760) · 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 O60760
- Elsewhere: RCSB PDB 4EE0 · PDBe 4EE0 · UniProt O60760
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