SMTL ID : 6i8y.1

Crystal structure of Spindlin1 in complex with the Methyltransferase inhibitor A366

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

2 x 2OD: 5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine(Non-covalent)

2OD.1: 8 residues within 4Å: Chain A: D.48, H.92, F.94, W.104, Y.123, Y.130, Y.132, D.137 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.94, A:F.94, A:W.104, A:W.104, A:W.104, A:Y.123, A:Y.132 Hydrogen bonds: A:Y.132, A:D.137 Water bridges: A:D.142 pi-Cation interactions: A:W.104 2OD.2: 11 residues within 4Å: Chain A: H.13, W.15, E.17, W.25, Y.44, F.47, Y.51, L.53, F.204 Ligands: EDO.3, MPD.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.15, A:W.15, A:W.25, A:W.25, A:Y.44, A:F.47, A:Y.51, A:F.204 pi-Cation interactions: A:Y.44

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

EDO.3: 4 residues within 4Å: Chain A: Y.51, F.204, H.205 Ligands: 2OD.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.51 EDO.4: 4 residues within 4Å: Chain A: L.166, K.169, F.221, Q.222 No protein-ligand interaction detected (PLIP)

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 4 residues within 4Å: Chain A: P.34, V.35, N.36, P.37 No protein-ligand interaction detected (PLIP)

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 5 residues within 4Å: Chain A: W.15, P.21, T.23, W.25 Ligands: 2OD.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.21

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 12 residues within 4Å: Chain A: G.106, M.107, T.122, Y.123, E.124, P.127, V.195, V.208, Y.209, D.210, K.213, S.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.122 Water bridges: A:S.215

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 2 residues within 4Å: Chain A: Q.170, Q.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.170, A:Q.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fagan, V. et al., A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function. J.Med.Chem. (2019)

Release Date

2018-12-26

Peptides

Spindlin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spindlin-1

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