SMTL ID : 6yx1.2 (1 other biounit)

Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x PWT: 2-[[2-(5-oxidanylidenepentanoyl)hydrazinyl]methyl]benzoic acid(Non-covalent)

PWT.1: 8 residues within 4Å: Chain A: V.27, L.28, R.29, G.30, H.85, R.86 Ligands: THR.2, ARG.3 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.27, A:R.29, A:R.86 Hydrogen bonds: A:G.30, R.3 Water bridges: A:Q.34, A:H.85

1 x THR: THREONINE(Non-covalent)

THR.2: 9 residues within 4Å: Chain A: V.27, L.28, H.85, R.86, V.89, R.93 Ligands: PWT.1, ARG.3, LEU.4 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.89 Hydrogen bonds: A:L.28, A:L.28, A:H.85, A:R.86, T.2

1 x ARG: ARGININE(Non-covalent)

ARG.3: 6 residues within 4Å: Chain A: F.26, V.27, D.56 Ligands: PWT.1, THR.2, LEU.4 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:V.27 Salt bridges: A:D.56

1 x LEU: LEUCINE(Non-covalent)

LEU.4: 7 residues within 4Å: Chain A: G.23, F.24, G.25, F.26, I.92 Ligands: THR.2, ARG.3 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:F.26, A:I.92 Hydrogen bonds: A:F.24, A:G.25, A:F.26, A:F.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hegedus, Z. et al., Identification of beta-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation. Chem Sci (2021)

Release Date

2021-01-20

Peptides

SH3 and multiple ankyrin repeat domains protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

SH3 and multiple ankyrin repeat domains protein 1

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