SMTL ID : 7xe1.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 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

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

FAD.4: 36 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 25 PLIP interactions: 25 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: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:Y.550 Salt bridges: A:R.391, A:R.391

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

DIJ.5: 7 residues within 4Å: Chain A: N.411, Y.516, K.632, Y.738, Q.774, T.775 Ligands: FAD.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.738, A:T.775 Hydrogen bonds: A:Y.516, A:K.632

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: H.457, A.460, L.461, V.464, F.491 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.457

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: L.701, Q.702, M.705, R.709, D.719, P.720 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.702, A:R.709, A:R.709 Water bridges: A:Q.702 GOL.8: 4 residues within 4Å: Chain A: I.484, E.485, L.507, Q.508 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.508 GOL.9: 5 residues within 4Å: Chain A: Q.112, R.119, W.121, E.160, V.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.112, A:E.160 GOL.10: 3 residues within 4Å: Chain A: C.436, F.651, Y.669 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.669

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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