SMTL ID : 6tuy.1

Human LSD1/CoREST bound to the quinazoline inhibitor MC4106

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

FAD.1: 39 residues within 4Å: Chain A: I.284, G.285, S.286, G.287, V.288, S.289, L.307, E.308, A.309, R.310, G.314, G.315, R.316, V.317, L.329, G.330, A.331, M.332, V.333, T.588, A.589, V.590, T.624, L.625, P.626, V.637, L.659, K.661, W.751, W.756, S.760, Y.761, G.800, E.801, A.809, T.810, V.811, A.814 Ligands: NY8.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.659 Hydrogen bonds: A:S.286, A:G.287, A:S.289, A:S.289, A:A.309, A:R.310, A:V.313, A:G.314, A:R.316, A:A.331, A:M.332, A:V.333, A:V.333, A:V.590, A:V.590, A:E.801, A:V.811 Water bridges: A:V.288, A:G.290, A:R.310, A:V.317 Salt bridges: A:R.316, A:R.316 pi-Stacking: A:Y.761

3 x NY8: ~{N}2-[3-(dimethylamino)propyl]-6,7-dimethoxy-~{N}4-[1-(naphthalen-2-ylmethyl)piperidin-4-yl]quinazoline-2,4-diamine(Non-covalent)

NY8.2: 15 residues within 4Å: Chain A: F.382, N.383, L.386, N.535, L.536, F.538, A.539, N.540, W.552, D.553, D.555, D.556, Y.761 Ligands: FAD.1, NY8.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.538, A:W.552 Hydrogen bonds: A:D.556 Salt bridges: A:D.555, A:D.556 NY8.3: 11 residues within 4Å: Chain A: Q.358, A.539, D.556, D.557, E.559, H.564, Y.761, A.809, T.810 Ligands: NY8.2, NY8.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.559, A:T.810 Hydrogen bonds: A:E.559 NY8.4: 4 residues within 4Å: Chain A: D.557, F.558, E.559 Ligands: NY8.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.558, A:F.558, A:E.559 Hydrogen bonds: A:E.559 Salt bridges: A:D.557

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 2 residues within 4Å: Chain A: K.469, P.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.469, A:P.471

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: P.471, R.472 Chain B: E.389 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: E.413, R.526, R.688 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: I.780 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: T.319 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: R.310, R.312 Ligands: GOL.11, DMS.12 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain A: R.310, D.754, W.756 Ligands: CL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.310

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.12: 7 residues within 4Å: Chain A: R.310, L.329, S.749, R.750, W.751, D.754 Ligands: CL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.750 Salt bridges: A:D.754 pi-Cation interactions: A:W.751

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Menna, M. et al., Novel non-covalent LSD1 inhibitors endowed with anticancer effects in leukemia and solid tumor cellular models. Eur.J.Med.Chem. (2022)

Release Date

2021-07-21

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

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