MolNFT v1 · #124764 · protein
Discovery of tak-272: a novel, potent and orally active renin in- hibitor
5KOT: “Discovery of tak-272: a novel, potent and orally active renin in- hibitor”. X-ray diffraction, 2 ligands (6VU, NAG), 6 pockets (best druggability 0.81). MolNFT v1 #124764 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KOT
- Type
- protein
- Length
- 665 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
- 6VU, NAG
- Pockets
- 6 · best druggability 0.81
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 | 332 | 16% helix, 46% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 333 | 17% helix, 47% strand | P00797 |
Ligands and binding sites
- 6VU · 1-(4-methoxybutyl)-~{N}-(2-methylpropyl)-~{N}-[(3~{S}, 5~{R})-5-morpholin-4-ylcarbonylpiperidin-3-yl]benzimidazole-2-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 · 14 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.81 | 0.86 | 67 | PGE, DMS |
| 2 | 503 | 0.73 | 0.81 | 45 | 6VU, PEG, DMS |
| 3 | 467 | 0.70 | 0.80 | 53 | 6VU, PEG, DMS |
| 4 | 272 | 0.56 | 0.77 | 32 | PEG |
| 5 | 156 | 0.49 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 833 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5KOT · Discovery of TAK-272: A Novel, Potent and Orally Active Renin In-hibitor · 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 5KOT · PDBe 5KOT · UniProt P00797
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.