MolNFT v1 · #113555 · protein
Complex of human hematopoietic prostagandin D2 synthase (hh- pgds) in complex with an active site inhibitor.
5AIX · Hematopoietic prostaglandin D synthase: “Complex of human hematopoietic prostagandin D2 synthase (hh- pgds) in complex with an active site inhibitor.”. X-ray diffraction, 3 ligands (GSH, KRX, MG), 6 pockets (best druggability 0.80).…
- PDB
- 5AIX
- 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, KRX, MG
- Pockets
- 6 · best druggability 0.80
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 · 2 copies · chains A, B, C, D
- KRX · 6-(3-methoxyphenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide · ligand · 2 copies · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.80 | 0.81 | 96 | GSH, KRX, MG |
| 2 | 1046 | 0.77 | 0.79 | 87 | MG, GSH, KRX |
| 3 | 463 | 0.71 | 0.82 | 66 | empty |
| 4 | 136 | 0.40 | 0.74 | 22 | empty |
| 5 | 71 | 0.31 | 0.74 | 13 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1435 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1415 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 329 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5AIX · Complex of human hematopoietic prostagandin D2 synthase (hH-PGDS) in complex with an… · 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 5AIX · PDBe 5AIX · UniProt O60760
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