SMTL ID : 6ywz.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 2.12 Å

Oligo State

monomer

Ligands

1 x PWN: 2-[(~{E})-(4-oxidanylidenebutanoylhydrazinylidene)methyl]benzoic acid(Non-covalent)

PWN.1: 8 residues within 4Å: Chain A: L.28, R.29, G.30, A.31, Q.50, G.84, H.85 Ligands: THR.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.30, A:Q.50, A:H.85, A:H.85, T.2

1 x THR: THREONINE(Non-covalent)

THR.2: 8 residues within 4Å: Chain A: V.27, L.28, H.85, V.89, R.93 Ligands: PWN.1, ARG.3, LEU.4 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: T.2, A:L.28, A:L.28, A:H.85

1 x ARG: ARGININE(Non-covalent)

ARG.3: 4 residues within 4Å: Chain A: F.26, D.56 Ligands: THR.2, LEU.4 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Water bridges: L.4 Salt bridges: A:D.56

1 x LEU: LEUCINE(Non-covalent)

LEU.4: 8 residues within 4Å: Chain A: G.23, F.24, G.25, F.26, I.92, R.93 Ligands: THR.2, ARG.3 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.26, A:F.26, A:I.92 Hydrogen bonds: A:F.24, A:G.25, A:F.26, A:F.26 Water bridges: R.3

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
A

SH3 and multiple ankyrin repeat domains protein 1

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