SMTL ID : 8sz3.1

Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 7j

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.94, C.96, C.125, N.127, Y.128 Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 12 residues within 4Å: Chain A: C.96, R.115, D.118, F.119, Y.122, Y.128, Y.213, R.214, T.216, F.218, N.219 Ligands: NAG-NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.128 Hydrogen bonds: A:D.118, A:Y.122, A:Y.128 NAG-NAG.5: 5 residues within 4Å: Chain B: N.94, C.96, C.125, N.127, Y.128 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 11 residues within 4Å: Chain B: C.96, R.115, D.118, F.119, Y.122, Y.128, Y.213, R.214, T.216, F.218, N.219 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.128 Hydrogen bonds: B:D.118, B:Y.128

2 x X18: N-[(1S)-1-(5-bromopyridin-2-yl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide(Non-covalent)

X18.3: 12 residues within 4Å: Chain A: R.115, K.149, S.150, L.151, D.215, T.216, F.217, L.220, K.223, D.245, D.246, K.288 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.151, A:F.217, A:D.245, A:K.288, A:K.288 Hydrogen bonds: A:D.215 Water bridges: A:T.216, A:F.217 X18.7: 13 residues within 4Å: Chain B: R.115, K.149, S.150, L.151, H.154, D.215, T.216, F.217, L.220, K.223, D.245, D.246, K.288 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.151, B:F.217, B:F.217, B:D.245 Hydrogen bonds: B:D.215, B:K.288

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

EDO.4: 4 residues within 4Å: Chain A: H.154, F.155, A.156, R.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.156, A:R.157 Water bridges: A:F.155 EDO.8: 3 residues within 4Å: Chain B: H.154, A.156, R.157 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:P.153, B:F.155 Hydrogen bonds: B:A.156, B:R.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jackson, J.J. et al., Imidazolone as an Amide Bioisostere in the Development of beta-1,3- N -Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors. J.Med.Chem. (2023)

Release Date

2023-12-06

Peptides

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2

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