SMTL ID : 7k41.1

Bacterial O-GlcNAcase (OGA) with compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 1 residues within 4Å: Chain A: W.403 No protein-ligand interaction detected (PLIP) ACT.12: 5 residues within 4Å: Chain A: R.101, N.199, E.202, V.203, D.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.204 Water bridges: A:N.199, A:F.205 Salt bridges: A:R.101

1 x VUA: 4-(4-methylpiperidin-1-yl)-N-(2-phenylethyl)pyrimidin-2-amine(Non-covalent)

VUA.2: 15 residues within 4Å: Chain A: G.138, Y.140, D.245, C.281, Y.285, T.313, V.317, I.318, W.340, N.342, D.347, Y.348, N.375, H.436 Ligands: EDO.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.285, A:Y.285, A:V.317, A:I.318, A:W.340, A:W.340, A:Y.348 Hydrogen bonds: A:D.347, A:N.375

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

EDO.3: 6 residues within 4Å: Chain A: D.265, A.269, Q.270, I.275, N.276, S.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.270, A:S.307 EDO.4: 7 residues within 4Å: Chain A: G.138, K.169, H.210, F.243, D.245, W.340 Ligands: VUA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.138, A:K.169, A:D.245 EDO.5: 5 residues within 4Å: Chain A: Y.140, D.347, R.350, Y.553, Q.554 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.350, A:Q.554 EDO.6: 4 residues within 4Å: Chain A: Y.140, G.141, R.350, Y.553 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.141, A:R.350, A:R.350 Water bridges: A:F.139, A:G.141, A:G.141 EDO.7: 4 residues within 4Å: Chain A: Y.359, G.360, Y.400, T.402 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.360, A:T.402 Water bridges: A:T.402 EDO.8: 3 residues within 4Å: Chain A: D.320, G.360, R.440 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.440 EDO.9: 4 residues within 4Å: Chain A: G.437, Y.438, R.439, R.440 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.437, A:R.439, A:R.440 EDO.10: 4 residues within 4Å: Chain A: P.433, N.434, G.437, R.439 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.434, A:N.434, A:R.439, A:R.439 EDO.11: 5 residues within 4Å: Chain A: S.7, Y.388, D.408, R.411, T.412 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.7, A:Y.388 Water bridges: A:Q.9, A:T.412 EDO.13: 5 residues within 4Å: Chain A: V.43, L.47, Q.108, A.111, K.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.108, A:Q.108, A:K.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tawada, M. et al., Discovery of a Novel and Brain-Penetrant O -GlcNAcase Inhibitor via Virtual Screening, Structure-Based Analysis, and Rational Lead Optimization. J.Med.Chem. (2021)

Release Date

2021-01-13

Peptides

O-GlcNAcase BT_4395: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O-GlcNAcase BT_4395