MolNFT v1 · #116429 · protein
Menin in complex with mi-2-3
5DDC: “Menin in complex with mi-2-3”. X-ray diffraction, 1 ligand (59V), 2 pockets (best druggability 0.65). MolNFT v1 #116429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DDC
- Type
- protein
- Length
- 465 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Menin
- UniProt
- O00255
- Ligands
- 59V
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Menin | protein | 465 | 58% helix, 5% strand | O00255 |
Ligands and binding sites
- 59V · 6-(2,2,2-trifluoroethyl)-4-{4-[5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl]piperazin-1-yl}thieno[2,3-d]pyrimidine · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · 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 | 577 | 0.65 | 0.76 | 63 | 59V, DMS |
| 2 | 54 | 0.29 | 0.76 | 20 | 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 5DDC · PDBe 5DDC · UniProt O00255
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