Research workbench
Ketopiperazine-based renin inhibitors: optimization of the "C" ring
Analyse Ketopiperazine-based renin inhibitors: optimization of the "C" ring in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G1Y
- Type
- protein
- Length
- 666 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
- 5IG, NAG
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renin (EC 3.4.23.15) | protein | 333 | 16% helix, 45% strand | P00797 |
Ligands and binding sites
- 5IG · 6-(2,4-diamino-6-ethylpyrimidin-5-yl)-4-(3-methoxypropyl)-2,2-dimethyl-2H-1,4-benzoxazin-3(4H)-one · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.75 | 0.82 | 57 | 5IG |
| 2 | 477 | 0.72 | 0.82 | 50 | 5IG |
| 3 | 116 | 0.42 | 0.76 | 21 | empty |
| 4 | 63 | 0.34 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2G1Y · Ketopiperazine-Based Renin Inhibitors: Optimization of the "C" Ring · 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 2G1Y · PDBe 2G1Y · UniProt P00797
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