SMTL ID : 7xw8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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 MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.516, A.518, S.519 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.519 MG.3: 3 residues within 4Å: Chain A: E.213, R.216, Q.251 No protein-ligand interaction detected (PLIP)

1 x FA8: [[(2R,3S,4S)-5-[(4AS)-7,8-DIMETHYL-2,4-DIOXO-4A,5-DIHYDROBENZO[G]PTERIDIN-10-YL]-2,3,4-TRIHYDROXY-PENTOXY]-HYDROXY-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL HYDROGEN PHOSPHATE(Non-covalent)

FA8.4: 38 residues within 4Å: Chain A: I.116, G.117, S.118, 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, K.493, W.583, W.588, S.592, Y.593, G.632, E.633, A.641, T.642, V.643, A.646 Ligands: I00.5 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:W.583 Hydrogen bonds: A:S.118, A:G.119, A:S.121, A:S.121, A:S.121, A:A.141, A:R.142, A:G.146, 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:G.122, A:R.142, A:G.147, A:R.148, A:V.149, A:R.423, A:K.493, A:K.493, A:H.634 Salt bridges: A:R.148, A:R.148 pi-Stacking: A:Y.593

1 x I00: ~{N}-(oxan-4-yl)-5-(3-oxidanylidenepropyl)thiophene-3-carboxamide(Non-covalent)

I00.5: 11 residues within 4Å: Chain A: V.165, T.167, I.188, F.370, A.371, H.396, L.509, W.527, Y.593, A.641 Ligands: FA8.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.527, A:Y.593

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hattori, Y. et al., Design, synthesis, and structure-activity relationship of TAK-418 and its derivatives as a novel series of LSD1 inhibitors with lowered risk of hematological side effects. Eur.J.Med.Chem. (2022)

Release Date

2022-10-12

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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