SMTL ID : 6i8b.2 (1 other biounit)

Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: P.34, V.35, P.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.34 Water bridges: A:P.34

1 x H7T: 2-[4-[2-[[2-[3-[2-azanyl-5-(cyclopropylmethoxy)-3,3-dimethyl-indol-6-yl]oxypropyl]-1,3-dihydroisoindol-5-yl]oxy]ethyl]-1,2,3-triazol-1-yl]-1-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]ethanone(Non-covalent)

H7T.2: 20 residues within 4Å: Chain A: H.13, W.15, W.25, Y.44, F.47, D.48, Y.51, L.53, H.92, M.93, F.94, E.95, W.104, Y.123, Y.130, Y.132, D.137, F.204, H.205 Ligands: DMS.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.15, A:W.25, A:W.25, A:W.25, A:F.47, A:Y.51, A:Y.51, A:F.94, A:F.94, A:W.104, A:W.104, A:Y.123, A:Y.132 Hydrogen bonds: A:Y.132, A:D.137 pi-Stacking: A:F.94 pi-Cation interactions: A:W.104

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

DMS.3: 5 residues within 4Å: Chain A: F.47, D.48, C.49, Y.51 Ligands: H7T.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.48, A:C.49, A:Y.51 Salt bridges: A:D.48

1 x GLY: GLYCINE(Non-covalent)

GLY.4: 6 residues within 4Å: Chain A: G.106, M.107, T.122, Y.123, E.124, D.210 4 PLIP interactions: 4 Ligand-Ligand interactions Hydrogen bonds: G.4, G.4, G.4, G.4

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

2018-12-05

Peptides

Spindlin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Spindlin-1

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