SMTL ID : 7xe2.1 (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: 6 residues within 4Å: Chain A: C.36, S.39, C.44, A.45, 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: 38 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, 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:Y.550, A:V.569, A:V.569, A:E.766, A:V.776 Water bridges: A:G.365, A:G.390, A:R.391, A:R.391, A:N.411, A:K.632, A:A.767, A:T.777 Salt bridges: A:R.391, A:R.391 pi-Stacking: A:Y.738, A:Y.738 FAD.6: 38 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, A.737, Y.738, G.765, E.766, Q.774, T.775, V.776, A.779 Ligands: FAD.4, DIJ.5, DIJ.7 27 PLIP interactions: 27 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:Y.550, A:V.569, A:V.569, A:E.766, A:V.776 Water bridges: A:G.365, A:G.390, A:R.391, A:R.391, A:N.411, A:T.777 Salt bridges: A:R.391, A:R.391

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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.738, A:Q.774, A:T.775 Hydrogen bonds: A:K.632 pi-Stacking: A:Y.738

1 x FLC: CITRATE ANION(Non-covalent)

FLC.8: 6 residues within 4Å: Chain A: Y.244, C.249, G.250, F.536, A.537, H.771 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.250, A:A.537 Water bridges: A:H.771, A:H.771 Salt bridges: A:H.771, A:H.771

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 4 residues within 4Å: Chain A: S.192, A.193, Y.195, C.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.194

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: D.573, S.575, N.611 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.575, A:S.575, A:N.611 Water bridges: A:G.576 GOL.11: 6 residues within 4Å: Chain A: L.461, I.484, E.485, Y.488, L.507, Q.508 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.485, A:E.485, A:Q.508 GOL.12: 7 residues within 4Å: Chain A: Y.173, L.176, I.177, L.178, P.179, R.273, D.274 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.173, A:Y.173, A:R.273 Water bridges: A:I.177, A:R.273, A:D.274 GOL.13: 3 residues within 4Å: Chain A: P.732, W.733, Q.735 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.735

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
A

Lysine-specific histone demethylase 1B

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