SMTL ID : 7cdg.1

Crystal structure of LSD1-CoREST in complex with PRSFLVRRR peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PRO- ARG- SER- PHE- LEU- VAL- ARG- ARG- ARG: PRO-ARG-SER-PHE-LEU-VAL-ARG-ARG-ARG(Non-covalent)

PRO-ARG-SER-PHE-LEU-VAL-ARG-ARG-ARG.1: 24 residues within 4Å: Chain A: T.171, Q.194, C.196, L.198, D.211, E.215, H.368, N.371, L.372, F.374, A.375, N.376, W.388, D.389, D.391, D.392, E.395, H.400, L.513, L.529, Y.597, A.645 Ligands: FAD.2, GOL.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.171, A:L.372, A:F.374, A:W.388, A:L.513, A:L.529, A:Y.597 Hydrogen bonds: A:Q.194, A:C.196, A:N.371, A:N.371, A:A.375 Salt bridges: A:D.211, A:E.215, A:E.215, A:D.389, A:D.392, A:E.395

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

FAD.2: 39 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, V.153, 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, K.497, W.587, W.592, S.596, Y.597, G.636, E.637, A.645, T.646, V.647, A.650 Ligands: PRO-ARG-SER-PHE-LEU-VAL-ARG-ARG-ARG.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.121, A:S.122, A:G.123, A:S.125, A:S.125, A:A.145, A:R.146, A:G.150, 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 Salt bridges: A:R.152, A:R.152 pi-Stacking: A:Y.597

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: G.245, E.249, I.252, R.362, F.369, L.380, R.524 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.362, A:R.524, A:R.524 GOL.4: 2 residues within 4Å: Chain A: K.210, S.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.210, A:S.358, A:S.358, A:R.360 GOL.5: 4 residues within 4Å: Chain A: 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.586, A:D.590 GOL.6: 5 residues within 4Å: Chain A: Q.194, H.400 Ligands: PRO-ARG-SER-PHE-LEU-VAL-ARG-ARG-ARG.1, PRO-ARG-SER-PHE-LEU-VAL-ARG-ARG-ARG.1, PRO-ARG-SER-PHE-LEU-VAL-ARG-ARG-ARG.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitagawa, H. et al., Structure-Based Identification of Potent Lysine-Specific Demethylase 1 Inhibitor Peptides and Temporary Cyclization to Enhance Proteolytic Stability and Cell Growth-Inhibitory Activity. J.Med.Chem. (2021)

Release Date

2021-06-23

Peptides

Lysine-specific histone demethylase 1A: A
REST corepressor 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific histone demethylase 1A

REST corepressor 1

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