MolNFT v1 · #92787 · protein
Crystal structure of renin in complex with nvp-BCA079 (compound 12A)
4GJ7: “Crystal structure of renin in complex with nvp-BCA079 (compound 12A)”. X-ray diffraction, 3 ligands (0LT, NAG, SO4), 6 pockets (best druggability 0.79). MolNFT v1 #92787 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GJ7
- Type
- protein
- Length
- 671 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
- 0LT, NAG, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Renin (EC 3.4.23.15) | protein | 335 | 14% helix, 45% strand | P00797 |
| B | Renin (EC 3.4.23.15) | protein | 336 | 16% helix, 44% strand | P00797 |
Ligands and binding sites
- 0LT · N-{[(3S,4S)-4-benzylpyrrolidin-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
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 | 475 | 0.79 | 0.87 | 65 | SO4 |
| 2 | 588 | 0.76 | 0.82 | 50 | 0LT |
| 3 | 724 | 0.74 | 0.79 | 68 | 0LT |
| 4 | 264 | 0.55 | 0.77 | 34 | empty |
| 5 | 228 | 0.53 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 850 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4GJ7 · Crystal structure of renin in complex with NVP-BCA079 (compound 12a) · 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 4GJ7 · PDBe 4GJ7 · UniProt P00797
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