MolNFT v1 · #59469 · protein
2-amino-1,3-thiazol-4(5H)-ones as potent and selective 11- hydroxysteroid dehydrogenase type 1 inhibitors
3BYZ · Corticosteroid 11-beta-dehydrogenase isozyme 1: “2-amino-1,3-thiazol-4(5H)-ones as potent and selective 11- hydroxysteroid dehydrogenase type 1 inhibitors”. X-ray diffraction, 2 ligands (NDP, H11), 13 pockets (best druggability…
- PDB
- 3BYZ
- Type
- protein
- Length
- 1,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Corticosteroid 11-beta-dehydrogenase isozyme 1
- EC
- 1.1.1.146
- UniProt
- P28845
- Ligands
- NDP, H11
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 258 | 50% helix, 14% strand | P28845 |
| B | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 255 | 52% helix, 16% strand | P28845 |
| C | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 255 | 52% helix, 16% strand | P28845 |
| D | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 261 | 51% helix, 15% strand | P28845 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- H11 · (5S)-2-(cyclooctylamino)-5-methyl-5-propyl-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
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.85 | 0.90 | 60 | NDP, H11 |
| 2 | 632 | 0.83 | 0.88 | 67 | NDP, H11 |
| 3 | 628 | 0.83 | 0.87 | 55 | NDP, H11 |
| 4 | 577 | 0.82 | 0.88 | 57 | NDP, H11 |
| 5 | 757 | 0.81 | 0.85 | 63 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2412 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2266 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 460 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 294 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3BYZ · 2-Amino-1,3-thiazol-4(5H)-ones as Potent and Selective 11-Hydroxysteroid Dehydrogenase… · 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 3BYZ · PDBe 3BYZ · UniProt P28845
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