MolNFT v1 · #63061 · protein
Further studies with the 2-amino-1,3-thiazol-4(5H)-one class of 11- hydroxysteroid dehydrogenase type 1 (11-HSD1) inhibitors: reducing pregnane X receptor (pxr) activity and exploring activity in a monkey pharmacodynamic model
3EY4 · 11-beta-hydroxysteroid dehydrogenase 1: “Further studies with the 2-amino-1,3-thiazol-4(5H)-one class of 11- hydroxysteroid dehydrogenase type 1…”. X-ray diffraction, 2 ligands (NDP, 352), 15 pockets (best druggability 0.85). MolNFT…
- PDB
- 3EY4
- Type
- protein
- Length
- 1,031 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 11-beta-hydroxysteroid dehydrogenase 1
- EC
- 1.1.1.146
- UniProt
- P28845
- Ligands
- NDP, 352
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 11-beta-hydroxysteroid dehydrogenase 1 (EC 1.1.1.146) | protein | 259 | 51% helix, 13% strand | P28845 |
| B | 11-beta-hydroxysteroid dehydrogenase 1 (EC 1.1.1.146) | protein | 255 | 47% helix, 16% strand | P28845 |
| C | 11-beta-hydroxysteroid dehydrogenase 1 (EC 1.1.1.146) | protein | 256 | 52% helix, 13% strand | P28845 |
| D | 11-beta-hydroxysteroid dehydrogenase 1 (EC 1.1.1.146) | protein | 261 | 50% helix, 15% strand | P28845 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, D, C
- 352 · (5S)-2-{[(1S)-1-(4-fluorophenyl)ethyl]amino}-5-(1-hydroxy-1-methylethyl)-5-methyl-1,3-thiazol-4(5H)-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.85 | 0.85 | 86 | NDP, 352 |
| 2 | 696 | 0.84 | 0.88 | 60 | NDP, 352 |
| 3 | 687 | 0.84 | 0.88 | 60 | NDP, 352 |
| 4 | 593 | 0.84 | 0.89 | 56 | NDP, 352 |
| 5 | 842 | 0.77 | 0.81 | 60 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2373 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2325 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 472 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 283 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 94 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3EY4 · Further studies with the 2-amino-1,3-thiazol-4(5H)-one class of 11-hydroxysteroid… · the same entry in another collection · chain D against D, TM-score 1.00
- P28845 · AlphaFold monomer V2.0 prediction for corticosteroid 11-beta- dehydrogenase isozyme 1… · a predicted model of the same protein · chain C against A, TM-score 1.00
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 P28845
- Elsewhere: RCSB PDB 3EY4 · PDBe 3EY4 · UniProt P28845
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