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Structural insights into the induced-fit inhibition of fascin by a small molecule

Analyse Structural insights into the induced-fit inhibition of fascin by a small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B0T
Type: protein
Length: 2,922 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fascin
UniProt: Q16658
Ligands: C7V
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Fascin	protein	487	7% helix, 46% strand	Q16658

Ligands and binding sites

C7V · 4-methyl-N-(1-{[4-(trifluoromethyl)phenyl]methyl}-1H-indazol-3-yl)-1,2-oxazole-5-carboxamide · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	812	0.73	0.78	99	C7V
2	255	0.65	0.82	38	C7V
3	337	0.65	0.80	47	C7V
4	267	0.64	0.81	30	C7V
5	211	0.63	0.83	33	C7V

Interfaces

8 interfaces between chains.

C–D · 394 Å² buried · 1 hydrogen bond · protein-protein
B–D · 370 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 358 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 322 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 225 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6B0T · Structural Insights into the Induced-fit Inhibition of Fascin by a Small Molecule · the same entry in another collection · chain F against F, TM-score 1.00
Q16658 · AlphaFold monomer V2.0 prediction for fascin (Q16658) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 Q16658
Elsewhere: RCSB PDB 6B0T · PDBe 6B0T · UniProt Q16658

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