SMTL ID : 6qpl.1

Crystal structure of Spindlin1 in complex with the inhibitor MS31

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

MPD.1: 12 residues within 4Å: Chain A: R.105, G.106, M.107, L.109, T.122, Y.123, E.124, P.127, V.195, V.208, Y.209, D.210 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.124, A:V.195, A:V.208, A:D.210 Water bridges: A:D.210 MPD.2: 8 residues within 4Å: Chain A: H.13, W.15, W.25, Y.44, F.47, Y.51, L.53, F.204 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.25, A:W.25, A:F.204, A:F.204 Hydrogen bonds: A:Y.51 Water bridges: A:Y.51

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

DMS.3: 3 residues within 4Å: Chain A: P.34, V.35, P.37 No protein-ligand interaction detected (PLIP) DMS.4: 4 residues within 4Å: Chain A: W.104, D.126, Y.130 Ligands: JC5.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.126

1 x JC5: [3-(aminomethyl)-5-[3-(1,3-dihydroisoindol-2-yl)propoxy]-4-methoxy-phenyl]methanamine(Non-covalent)

JC5.5: 10 residues within 4Å: Chain A: D.48, H.92, M.93, F.94, W.104, Y.123, Y.130, Y.132, D.137 Ligands: DMS.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.94, A:F.94, A:W.104, A:W.104, A:Y.123, A:Y.132 Hydrogen bonds: A:Y.132 Water bridges: A:G.46, A:D.48, A:D.142, A:D.142 pi-Cation interactions: A:W.104

1 x GLY: GLYCINE(Non-covalent)

GLY.6: 2 residues within 4Å: Chain A: R.144, P.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.144 Salt bridges: A:R.144

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 4 residues within 4Å: Chain A: E.54, K.57, D.58, R.60 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.54, A:R.60 Water bridges: A:E.54, A:E.54, A:E.59, A:K.199, A:K.199, A:D.201

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: D.177, G.178, S.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Y. et al., Discovery of a Potent and Selective Fragment-like Inhibitor of Methyllysine Reader Protein Spindlin 1 (SPIN1). J.Med.Chem. (2019)

Release Date

2019-07-17

Peptides

Spindlin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Spindlin-1

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