MolNFT v1 · #116428 · protein

Menin in complex with mi-319

5DDB: “Menin in complex with mi-319”. X-ray diffraction, 2 ligands (59Q, SO4), 2 pockets (best druggability 0.63). MolNFT v1 #116428 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DDB
Type: protein
Length: 463 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Menin
UniProt: O00255
Ligands: 59Q, SO4
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 59% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Menin	protein	463	59% helix, 5% strand	O00255

Ligands and binding sites

59Q · 4-{4-[5-(difluoromethyl)-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
PEG · Di(hydroxyethyl)ether · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	556	0.63	0.75	58	59Q, DMS
2	59	0.30	0.75	19	empty

Compared structures

5DDB · Menin in complex with MI-319 · the same entry in another collection · chain A against A, TM-score 1.00
O00255 · AlphaFold monomer V2.0 prediction for menin (O00255) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 5DDB · PDBe 5DDB · UniProt O00255

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