SMTL ID : 5l3e.1

LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: G.163, S.164, G.165, V.166, S.167, L.185, E.186, A.187, R.188, G.192, G.193, R.194, V.195, L.207, G.208, A.209, M.210, V.211, T.466, A.467, V.468, T.502, L.503, P.504, V.515, L.537, K.539, W.629, W.634, S.638, Y.639, G.678, E.679, A.687, T.688, V.689, A.692 Ligands: NA.7 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.164, A:G.165, A:V.166, A:S.167, A:S.167, A:A.187, A:R.188, A:G.192, A:R.194, A:V.195, A:A.209, A:M.210, A:V.211, A:V.211, A:V.468, A:V.468, A:E.679, A:V.689 Salt bridges: A:R.194, A:R.194 pi-Stacking: A:Y.639

5 x E11: N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine(Non-covalent)

E11.2: 14 residues within 4Å: Chain A: Q.236, N.261, L.264, N.413, L.414, F.416, A.417, W.430, D.431, D.433, D.434, H.442, W.573 Ligands: E11.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.430 Salt bridges: A:D.433 pi-Stacking: A:W.573 E11.3: 10 residues within 4Å: Chain A: Q.258, N.261, R.262, E.265, S.268, D.434, E.437 Ligands: E11.2, E11.4, E11.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.258, A:N.261, A:R.262 Hydrogen bonds: A:D.434 Salt bridges: A:E.265, A:E.265 E11.4: 9 residues within 4Å: Chain A: D.434, E.437, F.438, G.440, S.441, H.442 Ligands: E11.3, E11.5, E11.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.437 E11.5: 7 residues within 4Å: Chain A: D.435, F.436, E.437, F.438 Ligands: E11.3, E11.4, E11.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.436 Salt bridges: A:D.435 E11.6: 3 residues within 4Å: Chain A: G.440 Ligands: E11.4, E11.5 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: G.163, G.165, S.167, G.168, T.502 Ligands: FAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.165, A:S.167, A:S.167, A:G.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Speranzini, V. et al., Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features. Sci Adv (2016)

Release Date

2016-09-21

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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