SMTL ID : 8pd6.1

Crystal structure of the TRIM58 PRY-SPRY domain in complex with TRIM-473

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x YCB: ~{N}2-[3-(dimethylamino)propyl]-6-phenyl-~{N}4-(piperidin-4-ylmethyl)quinazoline-2,4-diamine(Non-covalent)

YCB.1: 13 residues within 4Å: Chain A: D.67, W.84, P.85, E.109, P.127, W.137, K.140, M.145, L.147, F.201, I.202, C.203 Ligands: CL.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.84, A:W.84, A:P.85, A:P.127, A:W.137, A:L.147, A:F.201, A:F.201 Hydrogen bonds: A:E.109 Water bridges: A:D.67, A:D.67 Salt bridges: A:E.109

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: E.106 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.106, H2O.2, H2O.4 MG.3: 5 residues within 4Å: Chain A: Q.116, D.117, T.118, G.194, L.195 No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: W.84, F.201 Ligands: YCB.1 Ligand excluded by PLIP

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

EDO.5: 7 residues within 4Å: Chain A: W.84, L.119, P.120, K.122, G.123, E.124, T.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.122, A:T.125 Water bridges: A:W.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoegenauer, K. et al., Discovery of Ligands for TRIM58, a Novel Tissue-Selective E3 Ligase. Acs Med.Chem.Lett. (2023)

Release Date

2024-01-31

Peptides

E3 ubiquitin-protein ligase TRIM58: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase TRIM58

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