Research workbench
Structure-based design of a new series of N-piperidin-3-ylpyrimidine- 5-carboxamides as renin inhibitors
Analyse Structure-based design of a new series of N-piperidin-3-ylpyrimidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SZ9
- Type
- protein
- Length
- 666 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
- 74Y, NAG
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 334 | 15% helix, 46% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 332 | 15% helix, 44% strand | P00797 |
Ligands and binding sites
- 74Y · (azepan-1-yl)(2-{[(furan-2-yl)methyl]amino}-6-methylpyridin-3-yl)methanone · 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 · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.83 | 0.88 | 63 | PEG |
| 2 | 608 | 0.75 | 0.81 | 54 | 74Y |
| 3 | 443 | 0.69 | 0.80 | 42 | 74Y |
| 4 | 265 | 0.55 | 0.77 | 34 | empty |
| 5 | 177 | 0.52 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1014 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5SZ9 · Structure-based design of a new series of N-piperidin-3-ylpyrimidine-5-carboxamides as… · 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 5SZ9 · PDBe 5SZ9 · UniProt P00797
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