MolNFT v1 · #106412 · protein
Renin in complexed with 4-methoxy-3-(3-methoxypropoxy)-N-{[(3S,4S)-4- {[(4-METHYLPHENYL)SULFONYL]AMINO}PYRROLIDIN-3-YL]METHYL}-N-(propan-2- YL)BENZAMIDE inhibitor
4RYC: “Renin in complexed with 4-methoxy-3-(3-methoxypropoxy)-N-{[(3S,4S)-4…”. X-ray diffraction, 3 ligands (3ZK, NAG, SO4), 6 pockets (best druggability 0.83). MolNFT v1 #106412 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4RYC
- Type
- protein
- Length
- 672 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
- 3ZK, NAG, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renin (EC 3.4.23.15) | protein | 336 | 15% helix, 46% strand | P00797 |
Ligands and binding sites
- 3ZK · 4-methoxy-3-(3-methoxypropoxy)-N-{[(3S,4S)-4-{[(4-methylphenyl)sulfonyl]amino}pyrrolidin-3-yl]methyl}-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
- DMS · Dimethyl sulfoxide · additive · 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 | 585 | 0.83 | 0.89 | 66 | SO4 |
| 2 | 609 | 0.75 | 0.82 | 56 | 3ZK |
| 3 | 576 | 0.75 | 0.82 | 45 | 3ZK, DMS |
| 4 | 278 | 0.56 | 0.77 | 35 | empty |
| 5 | 246 | 0.53 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 825 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4RYC · RENIN IN COMPLEXED WITH 4-methoxy-3-(3-methoxypropoxy)-N-{[(3S,4S)-4-{[(4-methylphenyl)sul… · 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 4RYC · PDBe 4RYC · UniProt P00797
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