SMTL ID : 5nps.1

The human O-GlcNAc transferase in complex with a bisubstrate inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

1 x ACE- VAL- THR- PRO- VAL- SER- THR- ALA- NH2: 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE(Non-covalent)

ACE-VAL-THR-PRO-VAL-SER-THR-ALA-NH2.1: 13 residues within 4Å: Chain A: H.183, H.185, H.186, N.244, H.245, P.246, Y.319, T.320, K.321, Q.526, F.555, V.582 Ligands: 94T.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.321, A:F.555 Hydrogen bonds: A:Y.319, A:K.321 Water bridges: A:Q.526, A:Q.526

1 x 94T: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] propyl hydrogen phosphate(Non-covalent)

94T.2: 20 residues within 4Å: Chain A: P.246, H.249, N.525, Q.526, K.529, L.553, V.582, A.583, K.585, H.588, R.591, G.606, H.607, T.608, T.609, D.612 Ligands: ACE-VAL-THR-PRO-VAL-SER-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-SER-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-SER-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-SER-THR-ALA-NH2.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.553 Hydrogen bonds: A:N.525, A:Q.526, A:A.583, A:A.583, A:K.585, A:K.585, A:H.588, A:R.591, A:H.607, A:T.608, A:T.608, A:T.609 Water bridges: A:K.585, A:K.585, A:T.609, A:T.609 Salt bridges: A:K.529, A:K.529 pi-Stacking: A:H.588

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rafie, K. et al., Thio-Linked UDP-Peptide Conjugates as O-GlcNAc Transferase Inhibitors. Bioconjug. Chem. (2018)

Release Date

2018-05-16

Peptides

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit