SMTL ID : 3abu.1

Crystal Structure of LSD1 in complex with a 2-PCPA derivative, S1201

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

1 x 12F: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3R,3aS)-3-[2-(benzyloxy)-3-fluorophenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate(Non-covalent)

12F.1: 41 residues within 4Å: Chain A: I.113, G.114, S.115, G.116, V.117, S.118, L.136, E.137, A.138, R.139, G.143, G.144, R.145, V.146, L.158, G.159, A.160, M.161, V.162, T.164, F.367, A.368, H.393, T.417, A.418, V.419, T.453, L.454, P.455, L.488, K.490, W.580, W.585, S.589, Y.590, G.629, E.630, A.638, T.639, V.640, A.643 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:R.145, A:F.367, A:F.367, A:A.368, A:W.580, A:Y.590, A:Y.590, A:Y.590, A:T.639 Hydrogen bonds: A:G.114, A:S.115, A:G.116, A:S.118, A:S.118, A:S.118, A:G.119, A:A.138, A:R.139, A:G.143, A:R.145, A:A.160, A:M.161, A:V.162, A:V.162, A:V.419, A:V.419, A:K.490, A:E.630, A:V.640 Salt bridges: A:R.145, A:R.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mimasu, S. et al., Structurally Designed trans-2-Phenylcyclopropylamine Derivatives Potently Inhibit Histone Demethylase LSD1/KDM1. Biochemistry (2010)

Release Date

2010-07-07

Peptides

Lysine-specific histone demethylase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific histone demethylase 1

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