SMTL ID : 7mlp.1

Crystal structure of ricin A chain in complex with 5-(2,6-dimethylphenyl)thiophene-2-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x ZJ4: 5-(2,6-dimethylphenyl)thiophene-2-carboxylic acid(Non-covalent)

ZJ4.1: 10 residues within 4Å: Chain A: Y.184, S.204, L.233, Q.234, R.235, R.236, F.241, I.248, L.249, I.252 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.184, A:L.233, A:L.249, A:I.252 Hydrogen bonds: A:R.236 Water bridges: A:N.237 Salt bridges: A:R.236 pi-Stacking: A:F.241

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: Q.161, L.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.162 EDO.3: 4 residues within 4Å: Chain A: L.134, R.135, I.206, N.210 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.210, A:N.210 Water bridges: A:R.135, A:R.135, A:R.135, A:R.135, A:R.135 EDO.4: 2 residues within 4Å: Chain A: E.139, R.198 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain A: N.11, E.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.11, A:E.62 EDO.6: 6 residues within 4Å: Chain A: E.147, A.148, T.164, R.167, S.168, I.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.167 Water bridges: A:E.147, A:A.151 EDO.7: 6 residues within 4Å: Chain A: T.14, G.16, A.17, H.66, N.142 Ligands: ZN.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:A.17, A:N.142

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 2 residues within 4Å: Chain A: H.66 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.66 ZN.9: 1 residues within 4Å: Chain A: H.41 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.41, H2O.8, H2O.9

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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