SMTL ID : 9dbp.1

Crystal structure of the LSD1/CoREST histone demethylase in complex with the cofactor FAD and the inhibitor GSK690

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

hetero-1-1-mer

Ligands

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

FAD.1: 42 residues within 4Å: Chain A: I.113, G.114, S.115, G.116, V.117, S.118, L.136, E.137, A.138, R.139, G.143, G.144, R.145, V.146, L.158, G.159, A.160, M.161, V.162, T.164, T.417, A.418, V.419, T.453, L.454, P.455, V.458, V.466, L.488, K.490, W.580, W.585, S.589, Y.590, G.629, E.630, A.638, T.639, V.640, H.641, A.643 Ligands: 01.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.488, A:L.488, A:Y.590 Hydrogen bonds: A:G.116, A:S.118, A:S.118, A:S.118, A:E.137, A:E.137, A:A.138, A:R.139, A:R.139, A:G.143, A:R.145, A:M.161, A:V.162, A:V.162, A:V.419, A:V.419, A:E.630, A:V.640 Salt bridges: A:R.145, A:R.145

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: G.238, L.241, E.242, I.245, R.355, F.362, L.373, T.514, R.517 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.355, A:R.355, A:R.517, A:R.517 GOL.3: 8 residues within 4Å: Chain A: R.139, R.141, A.147, L.158, S.578, R.579, W.580, D.583 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.139, A:R.141, A:R.579, A:R.579

1 x 01: 4-[2-(4-methylphenyl)-5-{[(3R)-pyrrolidin-3-yl]methoxy}pyridin-3-yl]benzonitrile

01.4: 19 residues within 4Å: Chain A: G.159, M.161, V.162, I.185, F.367, A.368, N.369, D.384, H.393, L.488, K.490, L.506, W.524, Y.590, S.591, P.637, A.638, T.639 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.162, A:F.367, A:L.506, A:W.524 Hydrogen bonds: A:K.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Novel, potent, and orally bioavailable LSD1 inhibitors induce fetal hemoglobin synthesis in a sickle cell disease mouse model. Blood (2025)

Release Date

2025-09-17

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