SMTL ID : 7e0g.1

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x HUF: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate(Non-covalent)

HUF.1: 36 residues within 4Å: Chain A: I.116, G.117, G.119, V.120, S.121, L.139, E.140, A.141, R.142, G.146, G.147, R.148, L.161, G.162, A.163, M.164, V.165, T.420, A.421, V.422, T.456, L.457, P.458, V.469, L.491, W.583, W.588, S.592, Y.593, G.632, E.633, A.641, T.642, V.643, A.646 Ligands: IMD.3 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:R.148, A:W.583, A:Y.593, A:Y.593 Hydrogen bonds: A:S.118, A:G.119, A:S.121, A:S.121, A:S.121, A:A.141, A:R.142, A:R.148, A:A.163, A:M.164, A:V.165, A:V.165, A:V.422, A:V.422, A:E.633, A:A.641, A:V.643 Water bridges: A:V.120, A:V.120, A:G.122, A:R.142, A:G.147, A:R.148, A:H.634 Salt bridges: A:R.148, A:R.148

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: G.241, E.245, I.248, R.358, L.376, T.517, R.520 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.358, A:R.358, A:R.520, A:R.520 Water bridges: A:S.377

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 7 residues within 4Å: Chain A: G.162, M.164, V.165, F.370, K.493, W.527 Ligands: HUF.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.164, A:K.493, A:K.493 IMD.4: 6 residues within 4Å: Chain A: C.192, L.194, D.207, E.211, W.363, H.364 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.211 pi-Stacking: A:H.364

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: T.516, A.518, S.519 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: E.213, R.216, Q.251 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baba, R. et al., LSD1 enzyme inhibitor TAK-418 unlocks aberrant epigenetic machinery and improves autism symptoms in neurodevelopmental disorder models. Sci Adv (2021)

Release Date

2021-03-24

Peptides

Lysine-specific histone demethylase 1A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific histone demethylase 1A

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