MolNFT v1 · #154605 · protein

LSD1-S2157 N5 adduct model

6KGP · Lysine-specific histone demethylase 1A: “LSD1-S2157 N5 adduct model”. X-ray diffraction, 2 ligands (DJ0, FAD), 6 pockets (best druggability 0.82). MolNFT v1 #154605 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KGP
Type: protein
Length: 647 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: DJ0, FAD
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific histone demethylase 1A (EC 1.-.-.-)	protein	647	46% helix, 18% strand	O60341

Ligands and binding sites

DJ0 · 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal · ligand · chains A
FAD · Flavin-adenine dinucleotide · ligand · chains A
GOL · Glycerol · additive · 6 copies · chains A
TLA · L(+)-tartaric acid · additive · chains A

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

Pockets

6 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	970	0.82	0.83	90	GOL, DJ0, FAD
2	303	0.60	0.78	29	empty
3	77	0.44	0.80	16	empty
4	138	0.41	0.74	28	TLA
5	79	0.39	0.78	21	GOL

Compared structures

6KGP · LSD1-S2157 N5 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 6KGP · PDBe 6KGP · UniProt O60341

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