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Human hematopoietic prostaglandin D synthase inhibitor complex structures
Analyse Human hematopoietic prostaglandin D synthase inhibitor complex structures in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VI5
- 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, M4M, CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 55% 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 | 55% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, D, B, C
- M4M · 1-amino-9,10-dioxo-4-[(4-sulfamoylphenyl)amino]-9,10-dihydroanthracene-2-sulfonic acid · ligand · 2 copies · chains C, A, D
- CA · Calcium ion · metal · 2 copies · chains B, C, A, D
- GOL · Glycerol · additive · chains 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 | 856 | 0.79 | 0.81 | 80 | GSH, CA, M4M |
| 2 | 953 | 0.73 | 0.77 | 57 | empty |
| 3 | 493 | 0.72 | 0.81 | 47 | CA, M4M |
| 4 | 396 | 0.70 | 0.81 | 40 | GSH |
| 5 | 121 | 0.67 | 0.89 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1444 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1429 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 320 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3VI5 · Human hematopoietic prostaglandin D synthase inhibitor complex structures · 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 3VI5 · PDBe 3VI5 · UniProt O60760
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