SMTL ID : 7mln.1

Crystal structure of ricin A chain in complex with 5-(o-tolyl)thiophene-2-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x ZJA: 5-(2-methylphenyl)thiophene-2-carboxylic acid(Non-covalent)

ZJA.1: 10 residues within 4Å: Chain A: Y.184, S.204, L.208, L.233, R.235, R.236, F.241, I.248, I.252 Ligands: GOL.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.184, A:L.208, A:L.233, A:I.248, A:I.252 Hydrogen bonds: A:R.236 Water bridges: A:N.237 Salt bridges: A:R.235 pi-Stacking: A:F.241

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: A.119, F.120, R.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.119, A:R.126 Water bridges: A:G.121 GOL.3: 2 residues within 4Å: Chain A: R.236 Ligands: ZJA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.236 GOL.4: 6 residues within 4Å: Chain A: T.14, G.16, A.17, N.142, I.193, N.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:I.193, A:N.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X.P. et al., Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design. J.Med.Chem. (2021)

Release Date

2022-02-09

Peptides

Ricin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ricin

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