Research workbench
Sortilin-progranulin interaction with compound 24
Analyse Sortilin-progranulin interaction with compound 24 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X4H
- Type
- protein
- Length
- 654 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin
- UniProt
- Q99523
- Ligands
- UOY, NAG
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin | protein | 654 | 6% helix, 39% strand | Q99523 |
Ligands and binding sites
- UOY · 4-methyl-N-(6-phenoxypyridine-3-carbonyl)-L-leucine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.62 | 0.77 | 60 | empty |
| 2 | 133 | 0.41 | 0.75 | 24 | NAG |
| 3 | 91 | 0.39 | 0.77 | 16 | UOY |
| 4 | 87 | 0.33 | 0.74 | 23 | GOL |
| 5 | 52 | 0.27 | 0.74 | 12 | empty |
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
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 6X4H · PDBe 6X4H · UniProt Q99523
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