SMTL ID : 6ywz.1 (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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 2 residues within 4Å: Ligands: ARG.4, LEU.5 No protein-ligand interaction detected (PLIP)

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

PWN.2: 7 residues within 4Å: Chain A: L.28, R.29, G.30, K.32, A.33, H.85 Ligands: THR.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.33 Hydrogen bonds: A:G.30, A:H.85

1 x THR: THREONINE(Non-covalent)

THR.3: 8 residues within 4Å: Chain A: V.27, L.28, H.85, V.89, R.93 Ligands: PWN.2, ARG.4, LEU.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:L.28, A:L.28, A:H.85, T.3 Hydrophobic interactions: L.5

1 x ARG: ARGININE(Non-covalent)

ARG.4: 6 residues within 4Å: Chain A: F.26, V.27, D.56 Ligands: PEG.1, THR.3, LEU.5 1 PLIP interactions: 1 interactions with chain A, Salt bridges: A:D.56

1 x LEU: LEUCINE(Non-covalent)

LEU.5: 10 residues within 4Å: Chain A: G.23, F.24, G.25, F.26, V.89, I.92, R.93 Ligands: PEG.1, THR.3, ARG.4 10 PLIP interactions: 2 Ligand-Ligand interactions, 8 interactions with chain A Hydrophobic interactions: T.3, A:F.26, A:V.89, A:I.92 Hydrogen bonds: L.5, A:F.24, A:G.25, A:F.26, 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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