SMTL ID : 8jf5.1

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAS1440

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 37 residues within 4Å: Chain A: G.115, S.116, G.117, V.118, S.119, L.137, E.138, A.139, R.140, G.144, G.145, R.146, V.147, L.159, G.160, A.161, M.162, V.163, T.418, A.419, V.420, T.454, L.455, P.456, V.467, L.489, W.581, W.586, S.590, Y.591, G.630, E.631, A.639, T.640, V.641, A.644 Ligands: UEU.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.489 Hydrogen bonds: A:S.116, A:V.118, A:S.119, A:G.120, A:E.138, A:A.139, A:R.140, A:G.144, A:R.146, A:V.147, A:A.161, A:M.162, A:V.163, A:V.163, A:V.420, A:V.420, A:E.631, A:V.641 Salt bridges: A:R.146, A:R.146 pi-Stacking: A:W.586, A:Y.591

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.243, F.363, T.515, R.518 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.518, A:R.518 GOL.3: 6 residues within 4Å: Chain A: R.140, R.142, S.579, R.580, W.581, D.584 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.140, A:R.142, A:S.579, A:D.584, A:D.584

1 x UEU: 4-[5-[(3~{R})-3-azanylpyrrolidin-1-yl]carbonyl-2-[2-fluoranyl-4-(2-methyl-2-oxidanyl-propyl)phenyl]phenyl]-2-fluoranyl-benzenecarbonitrile

UEU.4: 15 residues within 4Å: Chain A: M.162, V.163, T.165, N.365, F.368, A.369, D.385, H.394, K.491, L.507, L.523, W.525, Y.591, P.638 Ligands: FAD.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.163, A:T.165, A:F.368, A:W.525 Hydrogen bonds: A:N.365, A:A.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Machida, T. et al., TAS1440, a histone H3 competitive LSD1 inhibitor, activates both TGF-beta and notch signaling pathways via INSM1 dissociation in neuroendocrine small cell lung cancer. To Be Published

Release Date

2024-05-22

Peptides

Lysine-specific histone demethylase 1A: A
REST corepressor 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific histone demethylase 1A

REST corepressor 1