MolNFT v1 · #127263 · protein

Crystal structure of the VPS10P domain of human SORTILIN/NTS3 in complex with triazolone 18

5MRI: “Crystal structure of the VPS10P domain of human SORTILIN/NTS3 in complex with triazolone 18”. X-ray diffraction, 3 ligands (Q9Y, NAG, BMA), 6 pockets (best druggability 0.60). MolNFT v1 #127263 on GenesisL1: 3D structure, binding…

PDB: 5MRI
Type: protein
Length: 662 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sortilin
UniProt: Q99523
Ligands: Q9Y, NAG, BMA
Pockets: 6 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sortilin	protein	662	7% helix, 39% strand	Q99523

Ligands and binding sites

Q9Y · ~{N}-methyl-3-(3-methylbutyl)-5-oxidanyl-1,2,3-triazole-4-carboxamide · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
BMA · beta-D-mannopyranose · sugar

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	297	0.60	0.79	38	empty
2	175	0.47	0.76	35	empty
3	106	0.43	0.77	15	Q9Y
4	117	0.41	0.76	25	empty
5	51	0.28	0.75	15	empty

Modifications

Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5MRI · Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone… · the same entry in another collection · chain A against A, TM-score 1.00
Q99523 · AlphaFold monomer V2.0 prediction for sortilin (Q99523) · 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 Q99523
Elsewhere: RCSB PDB 5MRI · PDBe 5MRI · UniProt Q99523

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