SMTL ID : 7vqt.1

Crystal structure of LSD1 in complex with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: G.245, L.248, E.249, I.252, R.362, L.380, R.524 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.362, A:R.362, A:R.524, A:R.524 GOL.2: 5 residues within 4Å: Chain A: R.148, S.585, R.586, W.587, D.590 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.148, A:R.148, A:R.586 GOL.3: 4 residues within 4Å: Chain A: L.109, K.113, Q.134, G.417 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.113, A:K.113, A:Q.134 GOL.4: 5 residues within 4Å: Chain A: C.196, N.371, F.374, L.513, L.529 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.371

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

TLA.5: 6 residues within 4Å: Chain A: T.66, F.67, H.86, H.89, E.93, K.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.67, A:H.89 Salt bridges: A:H.86, A:H.89, A:K.107

1 x 7UW: 3-[3,5-bis(fluoranyl)-2-[(2-fluoranylpyridin-4-yl)methoxy]phenyl]propanal(Non-covalent)

7UW.6: 11 residues within 4Å: Chain A: G.166, M.168, V.169, F.374, L.495, K.497, W.531, L.542, Y.597, T.646 Ligands: FAD.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:M.168, A:F.374, A:L.495, A:Y.597 Hydrogen bonds: A:K.497, A:Y.597 pi-Stacking: A:W.531 Halogen bonds: A:K.497

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

FAD.7: 36 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, W.587, W.592, S.596, Y.597, G.636, E.637, A.645, T.646, V.647, A.650 Ligands: 7UW.6 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:R.152, A:W.587, A:Y.597 Hydrogen bonds: A:S.122, A:G.123, A:S.125, A:S.125, A:A.145, A:R.146, A:R.152, A:M.168, A:V.169, A:V.169, A:V.426, A:V.426, A:E.637, A:A.645, A:V.647 Salt bridges: A:R.152, A:R.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koda, Y. et al., Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles. Acs Med.Chem.Lett. (2022)

Release Date

2022-06-01

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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