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Crystal structure of SPINDLIN1 in complex with the inhibitor XY49-92B

Analyse Crystal structure of SPINDLIN1 in complex with the inhibitor XY49-92B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OCB
Type: protein
Length: 196 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spindlin-1
UniProt: Q9Y657
Ligands: V88, GLY, NA, PO4, CL
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Spindlin-1	protein	196	8% helix, 47% strand	Q9Y657

Ligands and binding sites

V88 · 7-[3-(1,3-dihydroisoindol-2-yl)propoxy]-2N-[2-(dimethylamino)ethyl]-6-methoxy-4N-(1-propan-2-ylpiperidin-4-yl)quinazoline-2,4-diamine · ligand · chains B
GLY · Glycine · ligand · chains B
NA · Sodium ion · metal · 2 copies · chains B
PO4 · Phosphate ion · ion · chains B
CL · Chloride ion · ion · chains B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B

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

Pockets

2 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	55	0.46	0.83	9	MPD
2	103	0.39	0.76	15	MPD

Compared structures

7OCB · Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B · the same entry in another collection · chain B against B, TM-score 1.00
Q9Y657 · AlphaFold monomer V2.0 prediction for spindlin-1 (Q9Y657) · 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 Q9Y657
Elsewhere: RCSB PDB 7OCB · PDBe 7OCB · UniProt Q9Y657

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