MolNFT v1 · #106416 · protein
Renin in complexed with N-({(3S,4S)-4-[(benzylsulfonyl) AMINO]PYRROLIDIN-3-YL}METHYL)-4-methoxy-3-(3-methoxypropoxy)-N- (propan-2-YL)BENZAMIDE inhibitor
4RYG: “Renin in complexed with N-({(3S,4S)-4-[(benzylsulfonyl) AMINO]PYRROLIDIN-3-YL}METHYL)-4-methoxy-3-(3-methoxypr…”. X-ray diffraction, 3 ligands (3ZJ, NAG, SO4), 6 pockets (best druggability 0.83). MolNFT v1 #106416 on GenesisL1: 3D…
- PDB
- 4RYG
- Type
- protein
- Length
- 673 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
- 3ZJ, NAG, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 336 | 15% helix, 46% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 337 | 16% helix, 45% strand | P00797 |
Ligands and binding sites
- 3ZJ · N-({(3S,4S)-4-[(benzylsulfonyl)amino]pyrrolidin-3-yl}methyl)-4-methoxy-3-(3-methoxypropoxy)-N-(propan-2-yl)benzamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains 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 | 576 | 0.83 | 0.89 | 68 | SO4 |
| 2 | 621 | 0.77 | 0.83 | 57 | 3ZJ |
| 3 | 550 | 0.73 | 0.81 | 52 | 3ZJ, DMS |
| 4 | 314 | 0.57 | 0.77 | 35 | empty |
| 5 | 282 | 0.56 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 845 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4RYG · RENIN IN COMPLEXED WITH N-({(3S,4S)-4-[(benzylsulfonyl)amino]pyrrolidin-3-yl}methyl)-4-met… · 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 4RYG · PDBe 4RYG · UniProt P00797
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