SMTL ID : 8tic.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 12 residues within 4Å: Chain A: C.96, E.97, R.115, D.118, F.119, Y.122, Y.128, Y.213, R.214, T.216, F.218, N.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.122, A:E.97, A:D.118, A:Y.122, A:Y.128 Hydrophobic interactions: A:Y.128 NAG-NAG-BMA-MAN-MAN.2: 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.122, B:D.118, B:Y.128, B:R.214 Hydrophobic interactions: B:Y.128

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

NAG.3: 4 residues within 4Å: Chain A: N.94, C.96, N.127, Y.128 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.128 Hydrogen bonds: A:N.94

2 x FKX: 3-(2-methylpropyl)-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxylic acid(Non-covalent)

FKX.4: 14 residues within 4Å: Chain A: K.149, S.150, L.151, H.154, D.215, T.216, F.217, L.220, K.223, D.245, D.246, D.247, K.288 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.217, A:D.245 Hydrogen bonds: A:D.215, A:K.223 Salt bridges: A:K.288 FKX.6: 13 residues within 4Å: Chain B: K.149, S.150, L.151, H.154, D.215, T.216, F.217, L.220, K.223, D.246, K.288 Ligands: GOL.7, GOL.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.151, B:F.217, B:F.217 Hydrogen bonds: B:D.215, B:K.223 Salt bridges: B:K.288

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: L.151, H.154, R.157 Ligands: FKX.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.157, A:R.157 GOL.7: 4 residues within 4Å: Chain B: L.151, H.154, R.157 Ligands: FKX.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.157, B:R.157 GOL.8: 8 residues within 4Å: Chain B: K.149, F.217, D.245, Y.289, G.306, D.332, D.333 Ligands: FKX.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.149, B:D.245, B:Y.289, B:G.306, B:D.332

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

CL.9: 4 residues within 4Å: Chain B: H.154, F.155, A.156, R.157 Ligand excluded by PLIP

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
C

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

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