Structure-based design of 7-azaindole-pyrrolidines as inhibitors of 11BETA-hydroxysteroid-dehydrogenase type I

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 16% strand (DSSP).

Ligands and binding sites

• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• 2M3 · 2-methyl-3-{(3S)-1-[(1-pyridin-2-ylcyclopropyl)carbonyl]pyrrolidin-3-yl}-1H-pyrrolo[2,3-b]pyridine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• SO4 · Sulfate ion · ion · 9 copies · chains B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• G–H · 2702 Ų buried · 29 hydrogen bonds · protein-protein
• C–D · 2662 Ų buried · 25 hydrogen bonds · protein-protein
• E–F · 2632 Ų buried · 20 hydrogen bonds · protein-protein
• A–B · 2610 Ų buried · 21 hydrogen bonds · protein-protein
• D–H · 497 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 3GMD · Structure-based design of 7-Azaindole-pyrrolidines as inhibitors of… · the same entry in another collection · chain H against H, 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 F 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 3GMD · PDBe 3GMD · UniProt P50172