MolNFT v1 · #170619 · protein
X-ray structure of furin in complex with the canavanine-based inhibitor 4-guanidinomethyl-phenylacetyl-canavanine-tle-canavanine- amba
6YD4: “X-ray structure of furin in complex with the canavanine-based inhibitor…”. X-ray diffraction, 6 ligands (2UE, 00S, CA), 4 pockets (best druggability 0.47). MolNFT v1 #170619 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6YD4
- Type
- protein
- Length
- 476 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Furin
- EC
- 3.4.21.75
- UniProt
- P09958
- Ligands
- 2UE, 00S, CA, NA, PO4, CL
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Furin (EC 3.4.21.75) | protein | 476 | 22% helix, 27% strand | P09958 |
Ligands and binding sites
- 2UE · 1-[4-(2-oxoethyl)benzyl]guanidine · ligand · chains A
- 00S · 4-(aminomethyl)benzenecarboximidamide · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.47 | 0.78 | 15 | empty |
| 2 | 66 | 0.33 | 0.76 | 17 | empty |
| 3 | 61 | 0.30 | 0.75 | 21 | empty |
| 4 | 50 | 0.23 | 0.72 | 13 | empty |
Modifications
Observed in the structure: 3 disulfide, 3 modified, 2 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
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 P09958
- Elsewhere: RCSB PDB 6YD4 · PDBe 6YD4 · UniProt P09958
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