SMTL ID : 5lhg.1

Structure of the KDM1A/CoREST complex with the inhibitor 4-methyl-N-[4-[[4-(1-methylpiperidin-4-yl)oxyphenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.34 Å

Oligo State

hetero-1-1-mer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: I.284, G.285, 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, W.751, W.756, S.760, Y.761, G.800, E.801, A.809, T.810, V.811, A.814 Ligands: 6X3.6 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:W.751, A:Y.761 Hydrogen bonds: A:G.287, A:S.289, A:S.289, A:S.289, A:A.309, A:R.310, A:G.314, A:R.316, A:M.332, A:V.333, A:V.333, A:V.590, A:V.590, A:E.801, A:A.809, A:V.811 Water bridges: A:V.288, A:G.290, A:R.310, A:G.315, A:R.316, A:R.316, A:K.661 Salt bridges: A:R.316, A:R.316

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.310, R.312, S.749, R.750, W.751, D.754 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.312, A:R.750 Water bridges: A:R.310, A:R.312 GOL.3: 6 residues within 4Å: Chain A: G.409, L.412, E.413, R.526, F.533, R.688 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.413, A:R.526, A:R.526, A:D.530 GOL.4: 5 residues within 4Å: Chain A: K.631, Q.652, R.653, M.654, G.655 No protein-ligand interaction detected (PLIP) GOL.5: 2 residues within 4Å: Chain A: W.646, L.775 No protein-ligand interaction detected (PLIP)

2 x 6X3: 4-methyl-N-[4-[[4-[(1-methyl-4-piperidyl)oxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide(Non-covalent)

6X3.6: 16 residues within 4Å: Chain A: V.333, T.335, Q.358, C.360, D.375, E.379, N.535, F.538, L.677, L.693, W.695, Y.761, A.809, T.810 Ligands: FAD.1, 6X3.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.333, A:Q.358, A:F.538, A:L.677, A:L.693, A:W.695 Salt bridges: A:D.375, A:E.379 6X3.7: 9 residues within 4Å: Chain A: Q.358, A.539, W.552, D.555, E.559, H.564, Y.761, A.809 Ligands: 6X3.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.539, A:A.809 Hydrogen bonds: A:Q.358 Salt bridges: A:E.559 pi-Stacking: A:H.564

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vianello, P. et al., Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure-Activity Relationship. J. Med. Chem. (2017)

Release Date

2017-02-22

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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