MolNFT v1 · #73718 · protein
Design and optimization of new piperidines as renin inhibitors
3OAD: “Design and optimization of new piperidines as renin inhibitors”. X-ray diffraction, 2 ligands (LPO, NAG), 3 pockets (best druggability 0.80). MolNFT v1 #73718 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OAD
- Type
- protein
- Length
- 669 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Renin
- EC
- 3.4.23.15
- UniProt
- P00797
- Ligands
- LPO, NAG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 162 | 14% helix, 49% strand | P00797 |
| B, D | Renin (EC 3.4.23.15) | protein | 171 | 16% helix, 43% strand | P00797 |
| C | Renin (EC 3.4.23.15) | protein | 165 | 14% helix, 48% strand | P00797 |
Ligands and binding sites
- LPO · (3S,4R)-N-[2-chloro-5-(2-methoxyethyl)benzyl]-N-cyclopropyl-4-{6-[2-(2,6-dichloro-4-methylphenoxy)ethoxy]pyridin-3-yl}-4-hydroxypiperidine-3-carboxamide · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.80 | 0.81 | 79 | LPO |
| 2 | 1145 | 0.78 | 0.80 | 103 | LPO |
| 3 | 53 | 0.29 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1942 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1909 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 628 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3OAD · Design and optimization of new piperidines as 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 3OAD · PDBe 3OAD · UniProt P00797
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