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Fragment-based discovery of mexiletine derivatives as orally bioavailable inhibitors of urokinase-type plasminogen activator

Analyse Fragment-based discovery of mexiletine derivatives as orally bioavailable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VIW
Type: protein
Length: 247 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urokinase-type plasminogen activator chain B
EC: 3.4.21.73
UniProt: P00749
Ligands: D56
Pockets: 1 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Urokinase-type plasminogen activator chain B (EC 3.4.21.73)	protein	247	11% helix, 41% strand	P00749

Ligands and binding sites

D56 · 4-(2-aminoethoxy)-N-(3-chloro-2-ethoxy-5-piperidin-1-ylphenyl)-3,5-dimethylbenzamide · ligand · chains A
ACT · Acetate ion · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	158	0.44	0.75	31	ACT, D56

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

2VIW · Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of… · 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 P00749
Elsewhere: RCSB PDB 2VIW · PDBe 2VIW · UniProt P00749

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