MolNFT v1 · #78645 · protein
Structure-based optimization of potent 4- and 6-azaindole-3- carboxamides as renin inhibitors
3SFC: “Structure-based optimization of potent 4- and 6-azaindole-3- carboxamides as renin inhibitors”. X-ray diffraction, 2 ligands (S53, NAG), 6 pockets (best druggability 0.82). MolNFT v1 #78645 on GenesisL1: 3D structure, binding sites…
- PDB
- 3SFC
- Type
- protein
- Length
- 680 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
- S53, NAG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renin (EC 3.4.23.15) | protein | 340 | 16% helix, 44% strand | P00797 |
Ligands and binding sites
- S53 · [7-benzyl-2-(5-fluoro-2-methylphenoxy)-1-phenyl-1H-pyrrolo[2,3-c]pyridin-3-yl](piperazin-1-yl)methanone · ligand · 3 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 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 | 453 | 0.82 | 0.90 | 61 | GOL |
| 2 | 575 | 0.75 | 0.82 | 61 | GOL, S53 |
| 3 | 587 | 0.74 | 0.81 | 53 | S53 |
| 4 | 266 | 0.60 | 0.80 | 37 | empty |
| 5 | 315 | 0.57 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1204 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3SFC · Structure-Based Optimization of Potent 4- and 6-Azaindole-3-Carboxamides as Renin… · 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 3SFC · PDBe 3SFC · UniProt P00797
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