MolNFT v1 · #124763 · protein
Discovery of tak-272: a novel, potent and orally active renin in- hibitor
5KOS: “Discovery of tak-272: a novel, potent and orally active renin in- hibitor”. X-ray diffraction, 2 ligands (6VS, NAG), 6 pockets (best druggability 0.81). MolNFT v1 #124763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KOS
- 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
- 6VS, NAG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 331 | 17% helix, 45% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 332 | 17% helix, 46% strand | P00797 |
Ligands and binding sites
- 6VS · 2-~{tert}-butyl-4-(3-methoxypropylamino)-~{N}-(2-methylpropyl)-~{N}-[(3~{S},5~{R})-5-morpholin-4-ylcarbonylpiperidin-3-yl]pyrimidine-5-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 · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.81 | 0.86 | 65 | DMS |
| 2 | 564 | 0.76 | 0.83 | 54 | 6VS, DMS |
| 3 | 481 | 0.73 | 0.82 | 45 | 6VS |
| 4 | 238 | 0.54 | 0.77 | 30 | empty |
| 5 | 135 | 0.50 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 867 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5KOS · Discovery of TAK-272: A Novel, Potent and Orally Active Renin In-hibitor · the same entry in another collection · chain B against B, 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 5KOS · PDBe 5KOS · UniProt P00797
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