MolNFT v1 · #60826 · protein
Crystal structure of human 11-beta-hydroxysteroid dehydrogenase (HSD1) in complex with benzamide inhibitor
3D3E · Corticosteroid 11-beta-dehydrogenase isozyme 1: “Crystal structure of human 11-beta-hydroxysteroid dehydrogenase (HSD1) in complex with benzamide inhibitor”. X-ray diffraction, 2 ligands (NAP, D3E), 16 pockets (best druggability…
- PDB
- 3D3E
- Type
- protein
- Length
- 1,039 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
- NAP, D3E
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 262 | 49% helix, 16% strand | P28845 |
| B, C, D | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 259 | 52% helix, 13% strand | P28845 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- D3E · N-cyclopropyl-N-(trans-4-pyridin-3-ylcyclohexyl)-4-[(1S)-2,2,2-trifluoro-1-hydroxy-1-methylethyl]benzamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.83 | 0.84 | 74 | NAP, D3E |
| 2 | 981 | 0.82 | 0.83 | 83 | NAP, D3E |
| 3 | 946 | 0.81 | 0.83 | 77 | NAP, D3E |
| 4 | 591 | 0.81 | 0.86 | 75 | empty |
| 5 | 833 | 0.79 | 0.82 | 70 | NAP, D3E |
Interfaces
6 interfaces between chains.
- A–B · 2219 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 2174 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 415 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 281 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 142 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3D3E · Crystal Structure of Human 11-beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with… · 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 D against A, TM-score 0.98
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 3D3E · PDBe 3D3E · UniProt P28845
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