SMTL ID : 5yj8.1

Identification of a small molecule inhibitor for the Tudor domain of TDRD3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x 8W9: 5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one(Non-covalent)

8W9.1: 5 residues within 4Å: Chain A: Y.18, Y.25, F.43, Y.46, N.48 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.18, A:Y.18, A:Y.25 Hydrogen bonds: A:N.48 pi-Stacking: A:Y.18, A:Y.46, A:Y.46

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: H.1, H.2, H.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.2, A:H.3, A:H.3 Salt bridges: A:H.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit. FEBS J. (2018)

Release Date

2018-05-02

Peptides

Tudor domain-containing protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tudor domain-containing protein 3