SMTL ID : 7khs.1 (1 other biounit)

OgOGA IN COMPLEX WITH LIGAND 55

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x WG4: N-(5-{[(5S)-7-(5-methylimidazo[1,2-a]pyrimidin-7-yl)-2,7-diazaspiro[4.4]nonan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide(Non-covalent)

WG4.1: 22 residues within 4Å: Chain A: G.10, F.11, Y.12, K.41, L.115, D.117, C.158, Y.162, T.193, I.197, V.198, W.221, N.223, A.226, D.228, Y.229, N.256 Chain B: F.369, H.385, N.386, W.389, F.424 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.369, B:F.424, A:Y.12, A:Y.162, A:I.197, A:W.221 pi-Stacking: B:W.389, B:W.389, A:Y.12 Hydrogen bonds: A:K.41, A:Y.162, A:N.223, A:N.256 Salt bridges: A:D.228 WG4.2: 21 residues within 4Å: Chain A: F.369, H.385, N.386, W.389, F.424 Chain B: G.10, F.11, Y.12, K.41, D.117, C.158, Y.162, T.193, I.197, V.198, W.221, N.223, A.226, D.228, Y.229, N.256 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.12, B:Y.162, B:I.197, B:W.221, B:Y.229, A:W.389, A:F.424 Hydrogen bonds: B:K.41, B:N.223, B:N.256 Salt bridges: B:D.228 pi-Stacking: B:Y.12, A:W.389, A:W.389

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain B: E.390, E.393, E.394 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.390, H2O.2, H2O.5, H2O.6, H2O.6, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Viturro, C.M. et al., Diazaspirononane Nonsaccharide Inhibitors of O-GlcNAcase (OGA) for the Treatment of Neurodegenerative Disorders. J.Med.Chem. (2020)

Release Date

2020-12-02

Peptides

Protein O-GlcNAcase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein O-GlcNAcase

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