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Xray structure of human furin bound with the 2,5-dideoxystreptamine derived small molecule inhibitor 1N

Analyse Xray structure of human furin bound with the 2,5-dideoxystreptamine derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MIM
Type: protein
Length: 473 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: 1N, NA, CA, CL
Pockets: 4 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Furin (EC 3.4.21.75)	protein	473	20% helix, 27% strand	P09958

Ligands and binding sites

1N · 1-[(1~{R},2~{R},4~{S},5~{S})-2,4-bis(4-carbamimidamidophenoxy)-5-[(4-carbamimidamidophenyl) amino]cyclohexyl]guanidine · ligand · 2 copies · chains A
NA · Sodium ion · metal · 4 copies · chains A
CA · Calcium ion · metal · 3 copies · chains A
CL · Chloride ion · ion · 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	121	0.46	0.78	14	empty
2	84	0.34	0.75	20	empty
3	55	0.32	0.77	15	empty
4	62	0.27	0.73	23	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5MIM · Xray structure of human furin bound with the 2,5-dideoxystreptamine derived small… · the same entry in another collection · chain A against A, TM-score 1.00
P09958 · AlphaFold monomer V2.0 prediction for furin (P09958) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 5MIM · PDBe 5MIM · UniProt P09958

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