MolNFT v1 · #90188 · protein
Crystal structure of hh-pgds with water displacing inhibitor
4EC0 · Hematopoietic prostaglandin D synthase: “Crystal structure of hh-pgds with water displacing inhibitor”. X-ray diffraction, 3 ligands (GSH, 7PQ, MG), 2 pockets (best druggability 0.78). MolNFT v1 #90188 on GenesisL1: 3D structure…
- PDB
- 4EC0
- Type
- protein
- Length
- 399 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, 7PQ, MG
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 54% 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 | 199 | 54% helix, 9% strand | O60760 |
| B | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 200 | 55% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B
- 7PQ · 4-[2-(aminomethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide · ligand · chains A
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.78 | 0.80 | 81 | GSH, MG, 7PQ |
| 2 | 92 | 0.52 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1423 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4EC0 · 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 4EC0 · PDBe 4EC0 · UniProt O60760
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