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
- 5SY3
- 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
- 74Z, NAG
- Pockets
- 7 · best druggability 0.82
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 | 333 | 16% helix, 46% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 335 | 16% helix, 44% strand | P00797 |
Ligands and binding sites
- 74Z · N-[(furan-2-yl)methyl]-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, A
- DMS · Dimethyl sulfoxide · additive · 12 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.82 | 0.87 | 66 | DMS |
| 2 | 562 | 0.75 | 0.82 | 62 | 1PE, DMS |
| 3 | 480 | 0.73 | 0.82 | 46 | 74Z, DMS |
| 4 | 171 | 0.53 | 0.79 | 29 | empty |
| 5 | 129 | 0.46 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 933 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5SY3 · 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 5SY3 · PDBe 5SY3 · UniProt P00797
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.