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X-ray structure of furin in complex with the canavanine-based inhibitor 4-aminomethyl-phenylacetyl-canavanine-tle-arg-amba

Analyse X-ray structure of furin in complex with the canavanine-based inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YD2
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: BVK, 00S, CA, NA, PO4, CL
Pockets: 4 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Furin (EC 3.4.21.75)	protein	476	21% helix, 27% strand	P09958

Ligands and binding sites

BVK · 2-[4-(aminomethyl)phenyl]ethanoic acid · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	130	0.45	0.77	14	empty
2	67	0.35	0.77	17	empty
3	77	0.32	0.75	26	empty
4	50	0.25	0.73	14	empty

Modifications

Observed in the structure: 3 disulfide, 2 covalent, 2 modified (disulfide, covalent ligand, nonstandard).

Compared structures

6YD2 · X-ray structure of furin in complex with the canavanine-based inhibitor… · the same entry in another collection · chain A against A, TM-score 0.99
P09958 · AlphaFold monomer V2.0 prediction for furin (P09958) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 6YD2 · PDBe 6YD2 · UniProt P09958

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