MolNFT v1 · #51226 · protein
Crystal structure of renin with inhibitor 3
2V16: “Crystal structure of renin with inhibitor 3”. X-ray diffraction, 1 ligand (C47), 5 pockets (best druggability 0.82). MolNFT v1 #51226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2V16
- Type
- protein
- Length
- 664 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
- C47
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Renin (EC 3.4.23.15) | protein | 333 | 12% helix, 44% strand | P00797 |
| O | Renin (EC 3.4.23.15) | protein | 331 | 9% helix, 45% strand | P00797 |
Ligands and binding sites
- C47 · Methyl (3R)-1-[(5S,6S,8R)-5-amino-9-butylamino-6-hydroxy-3,3,8-trimethyl-9-oxo-nonanoyl]-3,4-dihydro-2H-quinoline-3-carboxylate · ligand · 2 copies · chains C, O
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 | 913 | 0.82 | 0.84 | 83 | empty |
| 2 | 618 | 0.75 | 0.81 | 51 | C47 |
| 3 | 479 | 0.71 | 0.81 | 43 | C47 |
| 4 | 280 | 0.56 | 0.77 | 27 | empty |
| 5 | 290 | 0.55 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- C–O · 638 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2V16 · Crystal Structure of Renin with Inhibitor 3 · the same entry in another collection · chain C against C, 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 2V16 · PDBe 2V16 · UniProt P00797
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