MolNFT v1 · #124761 · protein
Discovery of tak-272: a novel, potent and orally active renin in- hibitor
5KOQ: “Discovery of tak-272: a novel, potent and orally active renin in- hibitor”. X-ray diffraction, 2 ligands (6VR, NAG), 6 pockets (best druggability 0.83). MolNFT v1 #124761 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KOQ
- 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
- 6VR, NAG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 335 | 16% helix, 46% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 333 | 16% helix, 45% strand | P00797 |
Ligands and binding sites
- 6VR · 2-~{tert}-butyl-4-(furan-2-ylmethylamino)-~{N}-(2-methylpropyl)-~{N}-[(3~{S})-piperidin-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
- 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 | 530 | 0.83 | 0.89 | 62 | empty |
| 2 | 583 | 0.75 | 0.82 | 67 | 6VR |
| 3 | 506 | 0.64 | 0.76 | 38 | 6VR |
| 4 | 160 | 0.53 | 0.80 | 23 | empty |
| 5 | 216 | 0.50 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5KOQ · 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 5KOQ · PDBe 5KOQ · UniProt P00797
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