SMTL ID : 6w4k.1

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with CC-90011

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

hetero-1-1-mer

Ligands

1 x V0Y: 4-[2-(4-aminopiperidin-1-yl)-5-(3-fluoro-4-methoxyphenyl)-1-methyl-6-oxo-1,6-dihydropyrimidin-4-yl]-2-fluorobenzonitrile(Non-covalent)

V0Y.1: 16 residues within 4Å: Chain A: M.159, V.160, T.162, I.183, Q.185, F.365, A.366, D.382, H.391, L.486, K.488, W.522, Y.588, P.635, A.636 Ligands: FAD.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.160, A:F.365, A:F.365, A:L.486, A:A.636 Hydrogen bonds: A:D.382

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

FAD.2: 37 residues within 4Å: Chain A: I.111, G.112, G.114, V.115, S.116, L.134, E.135, A.136, R.137, G.141, G.142, R.143, V.144, L.156, G.157, A.158, M.159, V.160, T.415, A.416, V.417, T.451, L.452, P.453, V.464, L.486, W.578, W.583, S.587, Y.588, G.627, E.628, A.636, T.637, V.638, A.641 Ligands: V0Y.1 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:Y.588 Hydrogen bonds: A:S.113, A:G.114, A:V.115, A:S.116, A:S.116, A:S.116, A:A.136, A:R.137, A:R.137, A:G.141, A:R.143, A:A.158, A:M.159, A:V.160, A:V.160, A:V.417, A:V.417, A:E.628, A:V.638 Water bridges: A:G.117, A:G.142, A:R.143, A:R.143, A:V.144, A:V.144 Salt bridges: A:R.143, A:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanouni, T. et al., Discovery of CC-90011: A Potent and Selective Reversible Inhibitor of Lysine Specific Demethylase 1 (LSD1). J.Med.Chem. (2020)

Release Date

2020-10-21

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