SMTL ID : 8fj4.1

LSD1-CoREST in complex with T108, short soaking

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

hetero-1-1-mer

Ligands

3 x XZU: 3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-phenylbenzamide

XZU.1: 11 residues within 4Å: Chain A: F.557, A.558, N.559, W.571, D.574, E.578, H.583, A.828 Ligands: XZU.2, XZU.3, XZQ.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.557, A:A.558, A:A.828 XZU.2: 10 residues within 4Å: Chain A: L.405, N.554, L.555, F.557, A.558, W.571, D.575 Ligands: XZU.1, XZU.3, XZQ.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.405, A:N.554, A:L.555, A:F.557, A:F.557, A:A.558, A:W.571, A:D.575 XZU.3: 7 residues within 4Å: Chain A: F.401, N.402, W.550, H.551, N.554 Ligands: XZU.1, XZU.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.402, A:W.550, A:W.550 Hydrogen bonds: A:N.402

1 x XZQ: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-[3-(phenylcarbamoyl)phenyl]-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate

XZQ.4: 45 residues within 4Å: Chain A: G.304, S.305, G.306, V.307, S.308, L.326, E.327, A.328, R.329, G.333, G.334, R.335, V.336, L.348, G.349, A.350, M.351, V.352, T.354, I.375, F.557, H.583, T.607, A.608, V.609, T.643, L.644, P.645, V.648, V.656, L.678, K.680, W.714, W.770, W.775, S.779, Y.780, G.819, E.820, A.828, T.829, V.830, A.833 Ligands: XZU.1, XZU.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:R.335, A:V.352, A:T.354, A:I.375, A:H.583, A:W.714, A:Y.780 Hydrogen bonds: A:S.305, A:G.306, A:S.308, A:S.308, A:G.309, A:A.328, A:R.329, A:R.335, A:A.350, A:M.351, A:V.352, A:V.352, A:V.609, A:V.609, A:K.680, A:E.820, A:A.828, A:V.830 Salt bridges: A:R.335, A:R.335 pi-Stacking: A:Y.780

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caroli, J. et al., Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1. to be published

Release Date

2024-06-26

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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