SMTL ID : 7w3l.1

Crystal structure of LSD1 in complex with cis-4-Br-2,5-F2-PCPA (S1024)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

monomer

Ligands

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

FAD.1: 37 residues within 4Å: Chain A: I.120, G.121, S.122, G.123, V.124, S.125, L.143, E.144, A.145, R.146, G.150, G.151, R.152, L.165, G.166, A.167, M.168, V.169, T.424, A.425, V.426, T.460, L.461, P.462, V.473, L.495, W.587, W.592, S.596, Y.597, G.636, E.637, A.645, T.646, V.647, A.650 Ligands: 8A2.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:W.587, A:Y.597 Hydrogen bonds: A:G.121, A:S.122, A:G.123, A:S.125, A:S.125, A:A.145, A:R.146, A:R.152, A:A.167, A:M.168, A:V.169, A:V.169, A:V.426, A:V.426, A:E.637, A:A.645, A:V.647 Water bridges: A:V.124, A:G.126, A:R.146, A:R.146, A:G.151, A:R.152, A:R.152, A:V.153 Salt bridges: A:R.152, A:R.152

1 x 8A2: 3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal(Non-covalent)

8A2.2: 10 residues within 4Å: Chain A: M.168, V.169, T.171, F.374, Y.597, P.644, A.645, T.646 Ligands: FAD.1, GOL.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.171, A:F.374, A:Y.597, A:Y.597 Halogen bonds: A:P.644

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.3: 6 residues within 4Å: Chain A: T.66, F.67, H.86, H.89, E.93, K.107 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.67, A:E.93 Water bridges: A:H.89, A:K.107, A:K.107 Salt bridges: A:H.86, A:H.89, A:K.107

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: G.245, L.248, E.249, I.252, R.362, F.369, L.380, T.521, R.524 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.362, A:R.362, A:R.524, A:R.524 Water bridges: A:S.381 GOL.5: 6 residues within 4Å: Chain A: R.146, R.148, S.585, R.586, W.587, D.590 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.146, A:R.148, A:R.148, A:R.586 GOL.6: 3 residues within 4Å: Chain A: K.113, Q.134, V.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.113, A:V.140, A:V.140 GOL.7: 4 residues within 4Å: Chain A: W.367, N.371, L.529, W.531 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.371, A:N.371 GOL.8: 2 residues within 4Å: Chain A: R.148, V.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.149 GOL.9: 9 residues within 4Å: Chain A: A.375, N.376, D.391, Y.597, S.598, Y.599, P.644, A.645 Ligands: 8A2.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.376, A:D.391 Water bridges: A:V.600, A:V.600

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 1A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific histone demethylase 1A

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