MolNFT v1 · #116426 · protein
Menin in complex with mi-326
5DD9: “Menin in complex with mi-326”. X-ray diffraction, 2 ligands (59K, SO4), 2 pockets (best druggability 0.62). MolNFT v1 #116426 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DD9
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Menin
- UniProt
- O00255
- Ligands
- 59K, SO4
- Pockets
- 2 · best druggability 0.62
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
- 59K · 4-[4-(5-methyl-1,3,4-thiadiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.62 | 0.75 | 56 | 59K, DMS |
| 2 | 70 | 0.32 | 0.75 | 21 | 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 5DD9 · PDBe 5DD9 · UniProt O00255
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