SMTL ID : 8r5c.1

Crystal structure of human TRIM7 PRYSPRY domain bound to (2-(1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x Y3C: (2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S})-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)-3-phenyl-propanoyl]amino]pentanoic acid(Non-covalent)

Y3C.1: 15 residues within 4Å: Chain A: R.18, T.46, N.47, T.48, R.49, G.72, W.73, A.74, L.87, F.90, Q.100, S.163, V.164, C.165 Ligands: SRT.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.48, A:A.74, A:L.87, A:F.90 Hydrogen bonds: A:T.48, A:T.48, A:G.72, A:S.163, A:S.163, A:C.165 Water bridges: A:F.90, A:N.102 Salt bridges: A:R.49

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

EDO.2: 3 residues within 4Å: Chain A: S.69, Y.106, H.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.69, A:Y.106, A:H.121 EDO.3: 6 residues within 4Å: Chain A: T.14, C.42, L.51, E.80, R.84, F.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.80, A:E.80, A:R.84, A:R.84 EDO.4: 4 residues within 4Å: Chain A: N.16, R.18, D.45, T.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16, A:N.16, A:R.18

2 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.5: 4 residues within 4Å: Chain A: F.56, S.57, S.58, H.61 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.57, A:S.58, A:H.61 Water bridges: A:G.55, A:S.58, A:H.61 Salt bridges: A:H.61, A:H.61 SRT.6: 3 residues within 4Å: Chain A: N.102, C.165 Ligands: Y3C.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:F.90, A:F.90, A:N.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Munoz Sosa, C.J. et al., A C-Degron Structure-Based Approach for the Development of Ligands Targeting the E3 Ligase TRIM7. Acs Chem.Biol. (2024)

Release Date

2024-01-17

Peptides

E3 ubiquitin-protein ligase TRIM7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase TRIM7

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