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Optimization of 3,5-disubstitued piperidine: discovery of non-peptide mimetics as an orally active renin inhibitor
Analyse Optimization of 3,5-disubstitued piperidine: discovery of non-peptide mimetics… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TMG
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Renin
- EC
- 3.4.23.15
- UniProt
- P00797
- Ligands
- 7EK, NAG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renin (EC 3.4.23.15) | protein | 334 | 16% helix, 46% strand | P00797 |
Ligands and binding sites
- 7EK · 5-(4-methoxybutyl)-N-(2-methylpropyl)-N-[(3S,5R)-5-(morpholine-4-carbonyl)piperidin-3-yl]-1-phenyl-1H-1, 2,3-triazole-4-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.82 | 0.88 | 64 | DMS |
| 2 | 578 | 0.73 | 0.80 | 50 | 7EK, PGE, DMS |
| 3 | 466 | 0.72 | 0.81 | 45 | 7EK |
| 4 | 195 | 0.53 | 0.78 | 28 | empty |
| 5 | 158 | 0.45 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1019 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5TMG · Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Peptide mimetics as an… · the same entry in another collection · 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 P00797
- Elsewhere: RCSB PDB 5TMG · PDBe 5TMG · UniProt P00797
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