SMTL ID : 6i8l.1

Crystal structure of Spindlin1 in complex with the inhibitor TD001851a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

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

MPD.1: 13 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, S.215 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.124, A:V.195, A:D.210 Water bridges: A:D.210, A:S.215, A:S.215, A:S.215

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.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.15, A:W.15, A:W.25, A:Y.44, A:Y.51, A:F.204

1 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)

1 x H7Q: 5'-(cyclopropylmethoxy)-6'-[3-(1,3-dihydroisoindol-2-yl)propoxy]spiro[cyclopentane-1,3'-indole]-2'-amine(Non-covalent)

H7Q.4: 10 residues within 4Å: Chain A: D.48, H.92, M.93, F.94, E.95, W.104, Y.123, Y.130, Y.132, D.137 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.94, 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-Cation interactions: A:W.104

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

CL.5: 1 residues within 4Å: Chain A: T.214 Ligand excluded by PLIP

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
B

Spindlin-1

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