SMTL ID : 5lhi.1

Structure of the KDM1A/CoREST complex with the inhibitor N-[3-(ethoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methylthieno[3,2-b]pyrrole-5-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

FAD.1: 37 residues within 4Å: Chain A: 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, W.751, W.756, S.760, Y.761, G.800, E.801, A.809, T.810, V.811, A.814 Ligands: 6X5.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.659, A:Y.761 Hydrogen bonds: A:S.286, A:G.287, A:S.289, A:S.289, A:S.289, A:A.309, A:R.310, A:R.310, 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:A.809, A:V.811 Water bridges: A:V.288, A:V.317 Salt bridges: A:R.316, A:R.316

1 x 6X5: ~{N}-[3-(ethoxymethyl)-2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide(Non-covalent)

6X5.2: 13 residues within 4Å: Chain A: V.333, I.356, Q.358, F.538, A.539, D.555, H.564, L.677, W.695, Y.761, A.809, T.810 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.333, A:I.356, A:A.539, A:L.677, A:W.695, A:Y.761 Hydrogen bonds: A:D.555

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: G.409, E.413, D.530, F.533, R.688 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.530, A:R.688, A:R.688 GOL.4: 7 residues within 4Å: Chain A: R.310, R.312, V.748, S.749, R.750, W.751, D.754 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.310, A:R.312, A:V.748, A:R.750, A:R.750

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 1: A
REST corepressor 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LYSINE-SPECIFIC HISTONE DEMETHYLASE 1

REST corepressor 1

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