MolNFT v1 · #134461 · protein
Novel approach of fragment-based lead discovery applied to renin inhibitors
5T4S: “Novel approach of fragment-based lead discovery applied to renin inhibitors”. X-ray diffraction, 2 ligands (77O, NAG), 7 pockets (best druggability 0.81). MolNFT v1 #134461 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5T4S
- 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
- 77O, NAG
- Pockets
- 7 · best druggability 0.81
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, 45% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 331 | 15% helix, 45% strand | P00797 |
Ligands and binding sites
- 77O · 6-chloro-N-[(furan-2-yl)methyl]pyrazin-2-amine · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains A
- PGE · Triethylene glycol · additive · chains 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 | 517 | 0.81 | 0.88 | 62 | DMS |
| 2 | 654 | 0.75 | 0.81 | 68 | PG6, DMS |
| 3 | 511 | 0.66 | 0.77 | 43 | 77O |
| 4 | 223 | 0.54 | 0.78 | 27 | empty |
| 5 | 91 | 0.45 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 886 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5T4S · Novel Approach of Fragment-Based Lead Discovery applied to 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 5T4S · PDBe 5T4S · UniProt P00797
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