SMTL ID : 9fyj.1

N-terminal domain of human galectin-8 in complex with an alpha-galactoside ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-dimer

Ligands

2 x 01: 2-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-5-oxidanyl-3-prop-2-ynoxy-oxan-4-yl]oxymethyl]-3-methyl-benzimidazole-5-carboxylic acid

01.1: 13 residues within 4Å: Chain A: R.42, Q.44, R.56, H.62, N.64, R.66, V.74, N.76, W.83, G.84, E.86, Y.138, G.139 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.83, A:Y.138 Hydrogen bonds: A:R.42, A:R.42, A:Q.44, A:R.56, A:R.56, A:N.64, A:R.66, A:N.76, A:E.86 Water bridges: A:R.66, A:G.139, A:G.139 01.3: 13 residues within 4Å: Chain B: R.42, Q.44, R.56, H.62, N.64, R.66, V.74, N.76, W.83, G.84, E.86, Y.138, G.139 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.83, B:Y.138 Hydrogen bonds: B:R.42, B:R.42, B:Q.44, B:R.56, B:R.56, B:N.64, B:R.66, B:N.76, B:G.139 Water bridges: B:R.66

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

CL.2: 7 residues within 4Å: Chain A: L.107, K.108, D.109, K.110 Chain B: I.127, G.128, K.131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Puric, E. et al., Nanomolar inhibitor of the galectin-8 N-terminal domain binds via a non-canonical cation-pi interaction. Commun Chem (2025)

Release Date

2025-03-12

Peptides

Isoform 1 of Galectin-8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 1 of Galectin-8