SMTL ID : 6kgr.1

LSD1-FCPA-MPE N5 adduct model

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

monomer

Ligands

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 5 residues within 4Å: Chain A: I.192, N.371, H.400, W.531 Ligands: DJC.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.192 Hydrogen bonds: A:N.371, A:H.400

1 x DJC: 3-[4-[5-fluoranyl-2-(trifluoromethyl)phenyl]phenyl]propanal(Non-covalent)

DJC.2: 11 residues within 4Å: Chain A: T.171, F.374, A.375, E.395, H.400, K.497, Y.597, A.645, T.646 Ligands: MPD.1, FAD.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.171, A:F.374, A:E.395, A:Y.597 Hydrogen bonds: A:K.497

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

FAD.3: 37 residues within 4Å: Chain A: I.120, G.121, S.122, G.123, V.124, S.125, L.143, E.144, A.145, R.146, G.150, G.151, R.152, 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: DJC.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:R.152, A:L.495, A:W.587, A:Y.597, A:Y.597 Hydrogen bonds: A:S.122, A:G.123, A:S.125, A:S.125, A:A.145, A:R.146, A:R.152, A:A.167, A:M.168, A:V.169, A:V.169, A:V.426, A:V.426, A:R.427, A:E.637, A:A.645, A:V.647 Water bridges: A:V.124, A:G.126, A:R.146, A:G.151, A:R.152, A:V.153, A:H.638 Salt bridges: A:R.152, A:R.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niwa, H. et al., Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Chemmedchem (2020)

Release Date

2020-03-25

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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