MolNFT v1 · #35716 · protein

LSD1-tranylcypromine complex

2EJR · Lysine-specific histone demethylase 1: “LSD1-tranylcypromine complex”. X-ray diffraction, 1 ligand (F2N), 5 pockets (best druggability 0.82). MolNFT v1 #35716 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2EJR
Type: protein
Length: 643 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific histone demethylase 1
EC: 1.-.-.-
UniProt: O60341
Ligands: F2N
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific histone demethylase 1 (EC 1.-.-.-)	protein	643	43% helix, 17% strand	O60341

Ligands and binding sites

F2N · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[7,8-dimethyl-2,4-dioxo-5-(3-phenylpropanoyl)-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 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	991	0.82	0.83	88	F2N
2	345	0.62	0.78	27	empty
3	113	0.49	0.80	21	empty
4	101	0.36	0.74	22	empty
5	59	0.27	0.73	12	empty

Compared structures

2EJR · LSD1-tranylcypromine complex · 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
Every structure of UniProt O60341
Elsewhere: RCSB PDB 2EJR · PDBe 2EJR · UniProt O60341

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