SMTL ID : 6te1.1

Structure of the KDM1A/CoREST complex with the inhibitor 2-[3-{4-chloro-3-[(4-chlorophenyl)ethynyl]phenyl}-1-(3-morpholin-4-ylpropyl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]-2-oxoethanol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

hetero-1-1-mer

Ligands

2 x N4K: 5-[4-cyclobutyl-1-[2-(4-piperidin-4-yloxyphenoxy)ethyl]imidazol-2-yl]-4-methyl-thieno[3,2-b]pyrrole(Non-covalent)

N4K.1: 18 residues within 4Å: Chain A: I.356, Q.358, C.360, E.379, W.531, H.532, N.535, L.536, F.538, A.539, N.540, W.552, D.556, H.564, L.677, L.693, W.695 Ligands: N4K.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.531, A:W.531, A:L.536, A:A.539, A:W.552, A:L.677, A:W.695 Hydrogen bonds: A:D.556 N4K.2: 17 residues within 4Å: Chain A: M.332, V.333, T.335, F.538, A.539, D.555, H.564, K.661, W.695, L.697, L.706, Y.761, P.808, A.809, T.810 Ligands: N4K.1, FAD.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.333, A:T.335, A:A.539, A:W.695, A:W.695, A:L.697, A:L.706 Hydrogen bonds: A:D.555 pi-Stacking: A:F.538

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

FAD.3: 36 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, 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: N4K.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.761 Hydrogen bonds: A:S.286, A:G.287, A:V.288, A:S.289, A:S.289, A:S.289, A:A.309, A:R.310, A:G.314, A:R.316, A:V.333, A:V.333, A:V.590, A:V.590, A:E.801, A:A.809, A:V.811 Water bridges: A:G.290, A:R.310, A:G.315, A:T.335, A:K.661 Salt bridges: A:R.316, A:R.316

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: R.310, R.312, V.748, S.749, R.750, W.751, D.754 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.310, A:R.312, A:R.750, A:W.751 GOL.5: 4 residues within 4Å: Chain A: R.312, A.318, L.329 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.312 GOL.6: 6 residues within 4Å: Chain A: G.409, E.413, R.526, F.533, L.544, R.688 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.526, A:R.526, A:R.688, A:R.688 GOL.7: 6 residues within 4Å: Chain A: K.631, Q.652, R.653, M.654, Y.763, A.765 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.631 GOL.8: 2 residues within 4Å: Chain A: L.775, Q.778 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romussi, A. et al., Discovery of Reversible Inhibitors of KDM1A Efficacious in Acute Myeloid Leukemia Models. Acs Med.Chem.Lett. (2020)

Release Date

2020-06-03

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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