Research workbench
Menin in complex with mi-859
Analyse Menin in complex with mi-859 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DDE
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Menin
- UniProt
- O00255
- Ligands
- 5A0, SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Menin | protein | 466 | 58% helix, 5% strand | O00255 |
Ligands and binding sites
- 5A0 · 6-(2,2-difluoroethyl)-4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]thieno[2,3-d]pyrimidine · ligand · 2 copies · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.63 | 0.75 | 53 | 5A0, DMS |
| 2 | 50 | 0.32 | 0.78 | 15 | empty |
| 3 | 59 | 0.29 | 0.75 | 19 | empty |
| 4 | 53 | 0.27 | 0.74 | 15 | empty |
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 O00255
- Elsewhere: RCSB PDB 5DDE · PDBe 5DDE · UniProt O00255
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