SMTL ID : 8tab.1

RTA-PD00589

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: R.186 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: A.115, F.116, R.122 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: F.89, R.111 Ligand excluded by PLIP

1 x U4T: 4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid(Non-covalent)

U4T.4: 9 residues within 4Å: Chain A: Y.180, Q.230, R.231, R.232, F.237, I.244, L.245, I.248 Ligands: EDO.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.180, A:F.237, A:I.244, A:L.245, A:I.248 Hydrogen bonds: A:R.232 Water bridges: A:R.232, A:N.233 Salt bridges: A:R.232

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

EDO.5: 3 residues within 4Å: Chain A: Y.180, G.183, E.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.180 Water bridges: A:E.184, A:R.232 EDO.6: 3 residues within 4Å: Chain A: R.231, F.237 Ligands: U4T.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.231, A:R.231

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.7: 5 residues within 4Å: Chain A: E.124, Q.125, G.128, N.129, L.130 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.J. et al., Structure-based design and optimization of a new class of small molecule inhibitors targeting the P-stalk binding pocket of ricin. Bioorg.Med.Chem. (2024)

Release Date

2024-05-01

Peptides

Ricin A chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ricin A chain

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