MolNFT v1 · #141125 · protein
Crystal structure of hematopoietic prostaglandin D synthase in complex with F092
5YWX: “Crystal structure of hematopoietic prostaglandin D synthase in complex with F092”. X-ray diffraction, 3 ligands (GSH, 93C, MG), 6 pockets (best druggability 0.77). MolNFT v1 #141125 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YWX
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- 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, 93C, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 198 | 57% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- 93C · N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl) pyrimidine-5-carboxamide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.77 | 0.79 | 90 | MG, GSH, 93C |
| 2 | 903 | 0.72 | 0.76 | 53 | GOL |
| 3 | 568 | 0.70 | 0.79 | 51 | GSH, 93C, MG |
| 4 | 518 | 0.67 | 0.78 | 40 | GSH, 93C |
| 5 | 133 | 0.61 | 0.85 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1412 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1383 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 328 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5YWX · Crystal structure of hematopoietic prostaglandin D synthase in complex with F092 · 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 5YWX · PDBe 5YWX · UniProt O60760
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