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Structure of spastin AAA domain in complex with a quinazoline-based inhibitor

Analyse Structure of spastin AAA domain in complex with a quinazoline-based inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NYV
Type: protein
Length: 283 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.425
Source: Drosophila melanogaster
Molecule: Spastin
EC: 5.6.1.1
UniProt: Q8I0P1
Ligands: LBD, SO4
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · resolution 2.425 · 1 distinct chain · 57% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Spastin (EC 5.6.1.1)	protein	283	57% helix, 10% strand	Q8I0P1

Ligands and binding sites

LBD · N-(3-tert-butyl-1H-pyrazol-5-yl)-2-[(2R)-2-methylpiperazin-1-yl]quinazolin-4-amine · ligand · chains B
SO4 · Sulfate ion · ion · chains B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.76	0.98	21	empty
2	185	0.51	0.77	28	LBD
3	106	0.50	0.81	20	empty

Compared structures

6NYV · Structure of spastin aaa domain in complex with a quinazoline-based inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
Q8I0P1 · AlphaFold monomer V2.0 prediction for spastin (Q8I0P1) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q8I0P1
Elsewhere: RCSB PDB 6NYV · PDBe 6NYV · UniProt Q8I0P1

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