SMTL ID : 6kgp.1

LSD1-S2157 N5 adduct model

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: G.245, L.248, E.249, I.252, R.362, F.369, L.380, R.524 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.362, A:R.362, A:R.524, A:R.524 GOL.2: 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.148, A:R.586 GOL.3: 2 residues within 4Å: Chain A: K.113, Q.134 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.113, A:K.113 Water bridges: A:Q.134, A:V.140 GOL.4: 6 residues within 4Å: Chain A: Q.194, C.196, W.367, N.371, F.374, L.529 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.194, A:N.371 GOL.5: 3 residues within 4Å: Chain A: R.148, V.149, V.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.149 GOL.6: 5 residues within 4Å: Chain A: C.196, D.211, E.215, W.367, H.368 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.196, A:D.211

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.7: 6 residues within 4Å: Chain A: T.66, F.67, H.86, H.89, E.93, K.107 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.67 Water bridges: A:L.65, A:E.68, A:H.89, A:H.89, A:E.93 Salt bridges: A:H.86, A:H.89, A:K.107

1 x DJ0: 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal(Non-covalent)

DJ0.8: 11 residues within 4Å: Chain A: M.168, V.169, T.171, F.374, A.375, H.400, Y.597, P.644, A.645, T.646 Ligands: FAD.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.374, A:F.374, A:F.374, A:A.375, A:Y.597, A:Y.597, A:T.646

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

FAD.9: 38 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, 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: DJ0.8 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:R.152, A:W.587 Hydrogen bonds: A:S.122, A:G.123, A:S.125, 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: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:R.152, A:V.153, A:T.460 Salt bridges: A:R.152, A:R.152 pi-Stacking: A:Y.597

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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