Research workbench
11-beta-HSD1 in complex with a 3,3-di-methyl-azetidin-2-one
Analyse 11-beta-HSD1 in complex with a 3,3-di-methyl-azetidin-2-one in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NMH
- Type
- protein
- Length
- 1,058 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
- P50172
- Ligands
- 2KG, NDP, SO4
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 265 | 50% helix, 15% strand | P50172 |
| B, D | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 264 | 51% helix, 15% strand | P50172 |
Ligands and binding sites
- 2KG · (4S)-4-(2-methoxyphenyl)-3,3-dimethyl-1-[3-(methylsulfonyl)phenyl]azetidin-2-one · ligand · 4 copies · chains A, B, C, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.84 | 0.87 | 76 | 2KG, NDP, SO4 |
| 2 | 730 | 0.84 | 0.87 | 63 | 2KG, NDP, SO4 |
| 3 | 720 | 0.84 | 0.87 | 64 | 2KG, NDP, SO4 |
| 4 | 775 | 0.83 | 0.86 | 64 | 2KG, NDP, SO4 |
| 5 | 416 | 0.68 | 0.80 | 65 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2662 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2641 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 365 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4NMH · 11-beta-HSD1 in complex with a 3,3-Di-methyl-azetidin-2-one · the same entry in another collection · chain D against D, TM-score 1.00
- P50172 · AlphaFold monomer V2.0 prediction for corticosteroid 11-beta- dehydrogenase isozyme 1… · a predicted model of the same protein · chain A 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 P50172
- Elsewhere: RCSB PDB 4NMH · PDBe 4NMH · UniProt P50172
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