SMTL ID : 7xe2.2 (1 other biounit)

Crystal structure of LSD2 in complex with trans-4-Br-PCPA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.113, C.118, C.140, C.156 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.113, A:C.118, A:C.140, A:C.156 ZN.2: 5 residues within 4Å: Chain A: C.24, C.29, H.55, S.57, H.61 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.24, A:C.29, A:H.55, A:H.61 ZN.3: 5 residues within 4Å: Chain A: C.36, S.39, C.44, C.63, C.66 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.36, A:C.44, A:C.63, A:C.66

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

FAD.4: 39 residues within 4Å: Chain A: I.359, G.360, G.362, P.363, A.364, L.382, E.383, A.384, K.385, G.389, G.390, R.391, R.405, G.406, A.407, Q.408, I.409, Y.550, P.568, V.569, T.597, V.598, P.599, I.608, I.630, W.728, W.733, I.734, A.737, Y.738, G.765, E.766, Q.774, T.775, V.776, A.779 Ligands: DIJ.5, FAD.6, DIJ.7 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:R.391, A:I.630, A:I.630, A:W.728, A:A.737 Hydrogen bonds: A:G.362, A:A.364, A:A.384, A:R.391, A:Q.408, A:I.409, A:I.409, A:V.569, A:V.569, A:E.766, A:Q.774, A:V.776 Water bridges: A:G.365, A:G.390, A:R.391, A:R.391, A:N.411, A:Y.550, A:K.632, A:A.767 Salt bridges: A:R.391, A:R.391 pi-Stacking: A:W.733, A:Y.738 FAD.6: 39 residues within 4Å: Chain A: I.359, G.360, G.362, P.363, A.364, L.382, E.383, A.384, K.385, G.389, G.390, R.391, R.405, G.406, A.407, Q.408, I.409, Y.550, P.568, V.569, T.597, V.598, P.599, I.608, I.630, W.728, W.733, I.734, A.737, Y.738, G.765, E.766, Q.774, T.775, V.776, A.779 Ligands: FAD.4, DIJ.5, DIJ.7 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:R.391, A:I.630, A:I.630, A:W.728, A:A.737 Hydrogen bonds: A:G.362, A:A.364, A:A.384, A:G.389, A:R.391, A:A.407, A:Q.408, A:I.409, A:I.409, A:V.569, A:V.569, A:E.766, A:Q.774, A:V.776 Water bridges: A:G.365, A:G.390, A:R.391, A:R.391, A:N.411, A:Y.550, A:K.632, A:A.767 Salt bridges: A:R.391, A:R.391 pi-Stacking: A:W.733

2 x DIJ: 3-(4-bromophenyl)propanal(Non-covalent)

DIJ.5: 9 residues within 4Å: Chain A: I.409, N.411, Y.516, Y.669, Y.738, Q.774 Ligands: FAD.4, FAD.6, DIJ.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.409, A:Y.516, A:Y.738 DIJ.7: 8 residues within 4Å: Chain A: N.411, K.632, Y.738, Q.774, T.775 Ligands: FAD.4, DIJ.5, FAD.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.738 Hydrogen bonds: A:K.632 pi-Stacking: A:Y.738

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: L.461, I.484, E.485, Y.488, L.507, Q.508 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.508

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niwa, H. et al., Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2. Acs Med.Chem.Lett. (2022)

Release Date

2022-09-14

Peptides

Lysine-specific histone demethylase 1B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Lysine-specific histone demethylase 1B

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