SMTL ID : 5yjb.1

LSD1-CoREST in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.96 Å

Oligo State

hetero-1-1-mer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: G.121, G.123, V.124, S.125, L.143, E.144, A.145, R.146, G.150, G.151, R.152, V.153, L.165, G.166, A.167, M.168, V.169, T.424, A.425, V.426, T.460, L.461, P.462, V.473, L.495, W.587, W.592, S.596, Y.597, G.636, E.637, A.645, T.646, V.647, A.650 Ligands: 8WC.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.495, A:Y.597 Hydrogen bonds: A:S.122, A:G.123, A:V.124, A:S.125, A:S.125, A:A.145, A:R.146, A:G.150, A:R.152, A:M.168, A:V.169, A:V.169, A:V.426, A:V.426, A:E.637, A:V.647 Salt bridges: A:R.152, A:R.152 pi-Stacking: A:W.592

1 x 8WC: 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile(Non-covalent)

8WC.2: 13 residues within 4Å: Chain A: M.168, V.169, F.374, A.375, N.376, D.391, L.495, K.497, L.513, W.531, Y.597, A.645 Ligands: FAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.169, A:F.374, A:L.495, A:L.513, A:W.531, A:A.645 Hydrogen bonds: A:D.391, A:K.497

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.245, R.362, T.521, R.524 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.362, A:R.524, A:R.524 GOL.4: 6 residues within 4Å: Chain A: R.146, R.148, S.585, R.586, W.587, D.590 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.146, A:R.148, A:R.586, A:D.590

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niwa, H. et al., Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile. Molecules (2018)

Release Date

2018-07-04

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

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