SMTL ID : 8f30.1

LSD1-CoREST in complex with AW2, long soaking

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x XB6: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)(Non-covalent)

XB6.1: 37 residues within 4Å: Chain A: G.304, S.305, G.306, V.307, S.308, 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, D.574, T.607, A.608, V.609, T.643, L.644, P.645, V.648, V.656, W.770, W.775, S.779, Y.780, G.819, E.820, A.828, T.829, V.830, A.833 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.780, A:T.829 Hydrogen bonds: A:S.305, A:V.307, A:S.308, A:S.308, A:A.328, A:R.335, A:M.351, A:V.352, A:V.352, A:V.609, A:V.609, A:K.680, A:W.775, 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

Waterbury, A.L. et al., Covalent adduct Grob fragmentation underlies LSD1 demethylase-specific inhibitor mechanism of action and resistance. Nat Commun (2025)

Release Date

2024-06-12

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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