SMTL ID : 8aak.1

Crystal structure of the PDZ tandem of syntenin in complex with compound 29

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x LL6: (2~{S})-2-[[(2~{S})-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)-3-phenyl-propanoyl]amino]propanoic acid(Non-covalent)

LL6.1: 10 residues within 4Å: Chain A: H.101, V.102, G.103, F.104, I.105, F.106, V.115, D.144, A.148, L.151 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:H.101, A:V.102, A:F.104, A:V.115, A:D.144, A:A.148, A:L.151 Hydrogen bonds: A:H.101, A:V.102, A:G.103, A:F.104, A:F.104, A:F.104, A:F.106 Salt bridges: A:H.101 pi-Stacking: A:H.101, A:F.106 LL6.2: 10 residues within 4Å: Chain B: H.101, V.102, G.103, F.104, I.105, F.106, V.115, D.144, A.148, L.151 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.101, B:F.104, B:I.105, B:F.106, B:V.115, B:D.144, B:A.148, B:L.151 Hydrogen bonds: B:V.102, B:G.103, B:F.104, B:F.104, B:F.106 Salt bridges: B:H.101 pi-Stacking: B:H.101, B:F.106

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain B: N.55, K.78 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoffer, L. et al., Discovery of a PDZ Domain Inhibitor Targeting the Syndecan/Syntenin Protein-Protein Interaction: A Semi-Automated "Hit Identification-to-Optimization" Approach. J.Med.Chem. (2023)

Release Date

2023-04-26

Peptides

Syntenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Syntenin-1

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