MolNFT v1 · #82805 · protein
Human renin in complex with inhibitor 7
3VYE: “Human renin in complex with inhibitor 7”. X-ray diffraction, 2 ligands (VYE, NAG), 6 pockets (best druggability 0.80). MolNFT v1 #82805 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VYE
- Type
- protein
- Length
- 670 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
- VYE, NAG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renin (EC 3.4.23.15) | protein | 335 | 15% helix, 45% strand | P00797 |
Ligands and binding sites
- VYE · (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-N-(3-methylbutyl)piperidine-3-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, 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 | 630 | 0.80 | 0.85 | 68 | empty |
| 2 | 603 | 0.74 | 0.81 | 54 | VYE |
| 3 | 560 | 0.73 | 0.81 | 49 | VYE |
| 4 | 327 | 0.55 | 0.75 | 33 | empty |
| 5 | 216 | 0.55 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3VYE · Human renin in complex with inhibitor 7 · 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 3VYE · PDBe 3VYE · UniProt P00797
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