SMTL ID : 7mlt.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: N.133, L.134, N.137 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Chain A: R.235 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: R.115 Ligand excluded by PLIP

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

EDO.4: 4 residues within 4Å: Chain A: I.9, I.10, A.28, R.32 Ligand excluded by PLIP EDO.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: H.95, P.96, N.98, Q.99 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: S.247, I.250 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: N.79, W.212, G.213, R.259 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: Q.129 Ligands: EDO.21 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: G.141, N.142, G.143, P.144, N.196, R.197, R.198 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: V.39, H.41, E.42, I.43, P.44 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: A.119, F.120, G.121, N.123, R.126 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: R.190 Ligands: EDO.17 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: E.62, S.70, V.71, T.72, R.86, A.87, G.88 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Q.161, L.162, P.163 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: N.24, R.27, A.28 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: Q.183, E.186, G.187, R.190 Ligands: EDO.13 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: N.137, I.138, E.139, R.167 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: E.147, T.164, R.167, S.168, I.171 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: E.136, A.200, P.201, D.202, P.203, I.206 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: Q.129 Ligands: EDO.9 Ligand excluded by PLIP

1 x ZJD: 5-(2-ethylphenyl)thiophene-2-carboxylic acid(Non-covalent)

ZJD.22: 8 residues within 4Å: Chain A: Y.184, L.208, L.233, Q.234, R.235, R.236, F.241, I.248 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.184, A:L.208, A:L.233, A:F.241, A:I.248 Hydrogen bonds: A:R.236 Water bridges: A:N.237 pi-Stacking: A:F.241

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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