MolNFT v1 · #108054 · protein

LSD1(KDM1A)-corest in complex with 1-benzyl-tranylcypromine

4UV8 · Lysine-specific histone demethylase 1A: “LSD1(KDM1A)-corest in complex with 1-benzyl-tranylcypromine”. X-ray diffraction, 1 ligand (D69), 10 pockets (best druggability 0.82). MolNFT v1 #108054 on GenesisL1: 3D structure, binding…

PDB: 4UV8
Type: protein
Length: 799 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific histone demethylase 1A; Rest corepressor 1
EC: 1.-.-.-
UniProt: O60341, Q9UKL0
Ligands: D69
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific histone demethylase 1A (EC 1.-.-.-)	protein	666	44% helix, 16% strand	O60341
B	Rest corepressor 1	protein	133	62% helix, 0% strand	Q9UKL0

Ligands and binding sites

D69 · [[(2R,3S,4S)-5-[(4aS,10aS)-4a-[(1S)-3-azanylidene-1,4-diphenyl-butyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-5,10a-dihydro-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentoxy]-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · chains A

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

Pockets

10 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	969	0.82	0.84	89	D69
2	345	0.61	0.78	32	empty
3	210	0.49	0.75	23	empty
4	96	0.44	0.79	19	empty
5	125	0.39	0.75	24	empty

Interfaces

1 interface between chains.

A–B · 2756 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

4UV8 · LSD1(KDM1A)-CoREST in complex with 1-Benzyl-Tranylcypromine · the same entry in another collection · chain A against A, TM-score 1.00
Q9UKL0 · AlphaFold monomer V2.0 prediction for rest corepressor 1 (Q9UKL0) · a predicted model of the same protein · chain B against A, TM-score 0.97

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
Every structure of UniProt Q9UKL0
Elsewhere: RCSB PDB 4UV8 · PDBe 4UV8 · UniProt O60341 · UniProt Q9UKL0

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