MolNFT v1 · #135026 · protein
Optimization of 3,5-disubstitued piperidine: discovery of non-peptide mimetics as an orally active renin inhibitor
5TMK: “Optimization of 3,5-disubstitued piperidine: discovery of non-peptide mimetics as an orally active renin…”. X-ray diffraction, 2 ligands (7EJ, NAG), 6 pockets (best druggability 0.79). MolNFT v1 #135026 on GenesisL1: 3D structure…
- PDB
- 5TMK
- Type
- protein
- Length
- 663 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
- 7EJ, NAG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 333 | 15% helix, 46% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 330 | 17% helix, 47% strand | P00797 |
Ligands and binding sites
- 7EJ · 1-(4-methoxybutyl)-N-(2-methylpropyl)-N-[(3S,5R)-5-(morpholine-4-carbonyl)piperidin-3-yl]-5-phenyl-1H-pyrrole-2-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.79 | 0.84 | 63 | DMS |
| 2 | 563 | 0.73 | 0.81 | 53 | 7EJ, DMS |
| 3 | 495 | 0.73 | 0.81 | 47 | 7EJ |
| 4 | 161 | 0.51 | 0.79 | 26 | empty |
| 5 | 212 | 0.50 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 821 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5TMK · 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 5TMK · PDBe 5TMK · UniProt P00797
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