SMTL ID : 8tjc.1

Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 8a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

1 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: 4 residues within 4Å: Chain A: N.94, C.96, N.127, Y.128 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.2: 12 residues within 4Å: Chain A: C.96, R.115, D.118, F.119, Y.122, Y.128, E.188, Y.213, R.214, T.216, F.218, N.219 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.128 Hydrogen bonds: A:D.118, A:Y.128, A:Y.122

1 x NAG- NAG- BMA- MAN: 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.3: 10 residues within 4Å: Chain B: 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.122

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.4: 13 residues within 4Å: Chain C: C.96, R.115, D.118, F.119, Y.122, Y.128, E.188, Y.213, R.214, T.216, F.218, N.219 Ligands: NAG.12 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.128 Hydrogen bonds: C:Y.122, C:Y.128, C:Y.122, C:E.188

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 11 residues within 4Å: Chain D: C.96, R.115, D.118, F.119, Y.122, Y.128, Y.213, R.214, T.216, F.218, N.219 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.118, D:Y.122, D:Y.128, D:R.214, D:Y.122

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 3 residues within 4Å: Chain A: D.245, D.247, H.376 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.376, H2O.1, H2O.2, H2O.2, H2O.2 MN.9: 3 residues within 4Å: Chain B: D.245, D.247, H.376 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.376 MN.13: 2 residues within 4Å: Chain C: D.247, H.376 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.247, C:H.376, H2O.4, H2O.4 MN.16: 3 residues within 4Å: Chain D: D.245, D.247, H.376 No protein-ligand interaction detected (PLIP)

4 x HI8: (6M)-1-[(2R)-3,3-dimethylbutan-2-yl]-6-[(5S)-5-methyl-4-oxo-5-phenyl-4,5-dihydro-1H-imidazol-2-yl]-1,3-dihydro-2H-benzimidazol-2-one(Non-covalent)

HI8.7: 11 residues within 4Å: Chain A: K.149, S.150, L.151, D.215, T.216, F.217, L.220, K.223, D.245, D.246, K.288 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.151, A:F.217, A:F.217, A:F.217, A:F.217, A:D.245, A:K.288 Hydrogen bonds: A:D.215 Water bridges: A:F.217, A:K.288, A:K.288 HI8.10: 11 residues within 4Å: Chain B: K.149, S.150, L.151, D.215, T.216, F.217, L.220, K.223, D.245, D.246, K.288 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.151, B:F.217, B:F.217, B:F.217, B:D.245 Hydrogen bonds: B:D.215, B:K.288 HI8.14: 11 residues within 4Å: Chain C: K.149, S.150, L.151, D.215, T.216, F.217, L.220, K.223, D.245, D.246, K.288 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.151, C:F.217, C:F.217, C:F.217, C:D.245, C:K.288 Hydrogen bonds: C:D.215, C:K.288 Water bridges: C:F.217 HI8.17: 11 residues within 4Å: Chain D: K.149, S.150, L.151, D.215, T.216, F.217, L.220, K.223, D.245, D.246, K.288 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.151, D:F.217, D:F.217, D:F.217, D:F.217, D:D.245, D:K.288 Hydrogen bonds: D:D.215, D:K.288 Water bridges: D:F.217

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

NAG.8: 4 residues within 4Å: Chain B: N.94, C.96, N.127, Y.128 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.128 Hydrogen bonds: B:N.94, B:N.127 NAG.12: 5 residues within 4Å: Chain C: N.94, C.96, N.127, Y.128 Ligands: NAG-NAG-BMA-MAN-MAN.4 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.128 Hydrogen bonds: C:N.127

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 4 residues within 4Å: Chain B: H.154, F.155, A.156, R.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.156, B:R.157, B:R.157 PEG.15: 5 residues within 4Å: Chain C: P.153, H.154, F.155, A.156, R.157 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.156, C:R.157 PEG.18: 5 residues within 4Å: Chain D: P.153, H.154, F.155, A.156, R.157 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.156, D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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