MolNFT v1 · #134234 · protein
Structure-based design of a new series of N-piperidin-3-ylpyrimidine- 5-carboxamides as renin inhibitors
5SY2: “Structure-based design of a new series of N-piperidin-3-ylpyrimidine- 5-carboxamides as renin inhibitors”. X-ray diffraction, 2 ligands (74V, NAG), 6 pockets (best druggability 0.82). MolNFT v1 #134234 on GenesisL1: 3D structure…
- PDB
- 5SY2
- Type
- protein
- Length
- 665 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
- 74V, NAG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 335 | 16% helix, 45% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 330 | 17% helix, 43% strand | P00797 |
Ligands and binding sites
- 74V · N-ethyl-4-{[(furan-2-yl)methyl]amino}-2-methyl-N-[(3S)-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
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
- 1PE · Pentaethylene glycol · 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 | 488 | 0.82 | 0.89 | 64 | DMS |
| 2 | 583 | 0.75 | 0.82 | 62 | 74V |
| 3 | 379 | 0.59 | 0.76 | 49 | 74V |
| 4 | 246 | 0.52 | 0.76 | 36 | empty |
| 5 | 154 | 0.51 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 971 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5SY2 · 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 5SY2 · PDBe 5SY2 · UniProt P00797
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