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LSD1-fcpa-mpe five-membered ring adduct model

Analyse LSD1-fcpa-mpe five-membered ring adduct model in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KGQ
Type: protein
Length: 651 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific histone demethylase 1A
EC: 1.-.-.-
UniProt: O60341
Ligands: DJC, FAD
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific histone demethylase 1A (EC 1.-.-.-)	protein	651	46% helix, 16% strand	O60341

Ligands and binding sites

DJC · 3-[4-[5-fluoranyl-2-(trifluoromethyl) phenyl]phenyl]propanal · ligand · chains A
FAD · Flavin-adenine dinucleotide · ligand · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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	897	0.82	0.84	92	MPD, DJC, FAD
2	302	0.61	0.79	27	empty
3	147	0.44	0.76	30	empty
4	71	0.40	0.79	17	empty
5	101	0.35	0.73	18	empty

Compared structures

6KGQ · LSD1-FCPA-MPE five-membered ring adduct model · 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 6KGQ · PDBe 6KGQ · UniProt O60341

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