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Crystallographic studies on the binding modes of P2-P3 butanediamide renin inhibitors
Analyse Crystallographic studies on the binding modes of P2-P3 butanediamide renin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BIM
- Type
- protein
- Length
- 667 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
- 0QB
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 334 | 12% helix, 43% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 333 | 14% helix, 42% strand | P00797 |
Ligands and binding sites
- 0QB · (2S)-2-[(2-amino-1,3-thiazol-4-yl)methyl]-N~1~-{(1S,2S)-1-(cyclohexylmethyl)-2-hydroxy-2-[(3R)-1,5,5-trimethyl-2-oxopyrrolidin-3-yl]ethyl}-N~4~-[2-(dimethylamino)-2-oxoethyl]-N~4~-[(1S)-1-phenylethyl]butanediamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.83 | 0.84 | 93 | empty |
| 2 | 630 | 0.76 | 0.82 | 57 | 0QB |
| 3 | 554 | 0.74 | 0.81 | 51 | 0QB |
| 4 | 113 | 0.42 | 0.77 | 22 | empty |
| 5 | 85 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1BIM · Crystallographic studies on the binding modes of P2-P3 butanediamide renin inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- P00797 · AlphaFold monomer V2.0 prediction for renin (P00797) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 1BIM · PDBe 1BIM · UniProt P00797
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