MolNFT v1 · #159444 · protein

Menin in complex with peptide inhibitor 25

6OPJ: “Menin in complex with peptide inhibitor 25”. X-ray diffraction, 2 ligands (ACE, SO4), 3 pockets (best druggability 0.73). MolNFT v1 #159444 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OPJ
Type: protein
Length: 479 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Menin; Peptide inhibitor 25
Ligands: ACE, SO4
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Menin	protein	467	57% helix, 5% strand	—
B	Peptide inhibitor 25	protein	12	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A
DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
PG4 · Tetraethylene glycol · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.73	0.85	37	empty
2	107	0.54	0.83	17	empty
3	70	0.39	0.79	19	empty

Interfaces

1 interface between chains.

A–B · 740 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified, 1 covalent (nonstandard, covalent ligand).

Compared structures

6OPJ · Menin in complex with peptide inhibitor 25 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6OPJ · PDBe 6OPJ

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