MolNFT v1 · #116432 · protein
Menin in complex with mi-273
5DDF: “Menin in complex with mi-273”. X-ray diffraction, 2 ligands (5A1, SO4), 3 pockets (best druggability 0.63). MolNFT v1 #116432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DDF
- Type
- protein
- Length
- 464 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Menin
- UniProt
- O00255
- Ligands
- 5A1, SO4
- Pockets
- 3 · 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 | 464 | 58% helix, 5% strand | O00255 |
Ligands and binding sites
- 5A1 · 4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(pentafluoroethyl)thieno[2,3-d]pyrimidine · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.63 | 0.76 | 53 | 5A1, DMS |
| 2 | 79 | 0.33 | 0.74 | 15 | empty |
| 3 | 66 | 0.28 | 0.74 | 16 | 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 5DDF · PDBe 5DDF · UniProt O00255
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