MolNFT v1 · #104138 · protein
Structure-based design of 4-hydroxy-3,5-substituted piperidines as direct renin inhibitors
4Q1N: “Structure-based design of 4-hydroxy-3,5-substituted piperidines as direct renin inhibitors”. X-ray diffraction, 3 ligands (2Y9, NAG, PO4), 6 pockets (best druggability 0.82). MolNFT v1 #104138 on GenesisL1: 3D structure, binding…
- PDB
- 4Q1N
- Type
- protein
- Length
- 672 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
- 2Y9, NAG, PO4
- Pockets
- 6 · 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 | 336 | 16% helix, 46% strand | P00797 |
Ligands and binding sites
- 2Y9 · (3S,4R,5R)-N-cyclopropyl-N'-[(2R)-1-ethoxy-4-methylpentan-2-yl]-4-hydroxy-N-[5-(propan-2-yl)pyridin-2-yl]piperidine-3,5-dicarboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- DMS · Dimethyl sulfoxide · 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 | 578 | 0.82 | 0.88 | 65 | empty |
| 2 | 574 | 0.74 | 0.81 | 63 | DMS, 2Y9 |
| 3 | 530 | 0.73 | 0.81 | 49 | DMS, 2Y9 |
| 4 | 292 | 0.57 | 0.77 | 35 | empty |
| 5 | 244 | 0.55 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 922 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4Q1N · Structure-based design of 4-hydroxy-3,5-substituted piperidines as direct renin inhibitors · 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 4Q1N · PDBe 4Q1N · UniProt P00797
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