MolNFT v1 · #69295 · protein
Optimization of orally bioavailable alkyl amine renin inhibitors
3KM4: “Optimization of orally bioavailable alkyl amine renin inhibitors”. X-ray diffraction, 2 ligands (22X, NAG), 3 pockets (best druggability 0.86). MolNFT v1 #69295 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KM4
- 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
- 22X, NAG
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 337 | 15% helix, 46% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 333 | 16% helix, 46% strand | P00797 |
Ligands and binding sites
- 22X · (3R)-3-[(1S)-4-(acetylamino)-1-(3-chlorophenyl)-1-hydroxybutyl]-N-{(1S)-2-cyclohexyl-1-[(methylamino)methyl]ethyl}piperidine-1-carboxamide · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.86 | 0.87 | 105 | 22X |
| 2 | 76 | 0.51 | 0.84 | 20 | empty |
| 3 | 63 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1037 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3KM4 · Optimization of Orally Bioavailable Alkyl Amine 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 3KM4 · PDBe 3KM4 · UniProt P00797
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