SMTL ID : 6k3e.1

LSD1/Co-Rest structure with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CW0: piperidin-4-ylmethyl 4-fluoranyl-4-[[[(1~{R},2~{S})-2-phenylcyclopropyl]amino]methyl]piperidine-1-carboxylate(Non-covalent)

CW0.1: 12 residues within 4Å: Chain A: N.364, F.367, A.368, N.369, W.381, D.384, H.393, L.506, W.524, S.591, A.638 Ligands: D3U.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.506, A:A.638

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.2: 6 residues within 4Å: Chain A: C.24, H.88, D.656, A.661, M.662 Ligands: CL.29 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: E.242, R.355, R.517 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.242 Hydrogen bonds: A:R.355 Salt bridges: A:R.517 ACT.4: 3 residues within 4Å: Chain A: K.250, D.254 Chain B: E.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.250

3 x MLA: MALONIC ACID(Non-covalent)

MLA.5: 6 residues within 4Å: Chain A: R.139, R.141, S.578, R.579, W.580, D.583 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.579, A:D.583, A:D.583, A:D.583 Salt bridges: A:R.139, A:R.141 MLA.6: 4 residues within 4Å: Chain A: W.475, L.604, Q.607 Ligands: EDO.20 No protein-ligand interaction detected (PLIP) MLA.7: 3 residues within 4Å: Chain A: K.203, S.351, R.353 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.351, A:S.351 Salt bridges: A:K.203, A:R.353

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: R.11, L.645 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.11, A:R.11 GOL.9: 9 residues within 4Å: Chain A: T.425, S.427, G.428, C.429, E.430, K.446 Ligands: GOL.10, GOL.11, EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.425, A:E.430 GOL.10: 2 residues within 4Å: Ligands: GOL.9, GOL.11 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain A: T.425, S.427, S.614 Ligands: GOL.9, GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.425, A:S.427, A:S.427, A:S.614

1 x D3U: 2-PCPA derivative(Non-covalent)

D3U.12: 38 residues within 4Å: Chain A: G.114, S.115, G.116, V.117, S.118, L.136, E.137, A.138, R.139, G.143, G.144, R.145, V.146, L.158, G.159, A.160, M.161, V.162, T.164, T.417, A.418, V.419, T.453, L.454, P.455, V.466, L.488, W.580, W.585, S.589, Y.590, G.629, E.630, A.638, T.639, V.640, A.643 Ligands: CW0.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:T.164, A:Y.590, A:Y.590, A:T.639 Hydrogen bonds: A:S.115, A:G.116, A:V.117, A:S.118, A:S.118, A:A.138, A:R.139, A:R.139, A:R.145, A:M.161, A:V.162, A:V.162, A:V.419, A:V.419, A:E.630, A:V.640 Water bridges: A:R.145, A:R.145 Salt bridges: A:R.145, A:R.145 pi-Stacking: A:W.585, A:Y.590

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 2 residues within 4Å: Chain A: T.442, I.444 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.444, A:I.444 EDO.14: 5 residues within 4Å: Chain A: Q.20, H.88, R.649, G.652, R.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.20, A:H.88 EDO.15: 3 residues within 4Å: Chain A: H.223, D.382, D.386 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.382 EDO.16: 1 residues within 4Å: Chain A: F.8 No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain A: N.546, S.548, R.579 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.579 EDO.18: 6 residues within 4Å: Chain A: S.427, G.428, C.429, K.446, C.447 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.429 EDO.19: 1 residues within 4Å: Chain A: P.470 No protein-ligand interaction detected (PLIP) EDO.20: 4 residues within 4Å: Chain A: W.475, P.608, T.610 Ligands: MLA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.608, A:T.610 EDO.21: 4 residues within 4Å: Chain A: D.603, Q.607, R.649, R.653 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.603, A:R.653, A:R.653 EDO.22: 1 residues within 4Å: Chain A: G.562 No protein-ligand interaction detected (PLIP) EDO.23: 3 residues within 4Å: Chain A: F.8, L.12, P.13 No protein-ligand interaction detected (PLIP) EDO.24: 2 residues within 4Å: Chain A: Q.187, G.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.187, A:G.391

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

PEG.25: 1 residues within 4Å: Chain A: D.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.27, A:D.27 PEG.26: 3 residues within 4Å: Chain A: G.410, L.411, D.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.410 PEG.27: 2 residues within 4Å: Chain A: D.382, D.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.382

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.28: 1 residues within 4Å: Chain A: Q.481 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Ligands: DTT.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J., LSD1/Co-Rest structure with an inhibitor. To Be Published

Release Date

2020-05-20

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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