SMTL ID : 7khv.1 (2 other biounits)

CpOGA IN COMPLEX WITH LIGAND 54

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x X1A: N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide(Non-covalent)

X1A.1: 22 residues within 4Å: Chain A: G.157, F.158, Y.159, K.188, D.267, N.268, C.301, Y.305, T.336, V.340, V.341, W.364, N.366, V.369, D.371, Y.372, K.374, N.399, W.460 Chain B: T.592, L.593, I.594 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.267, A:Y.305, A:T.336, A:W.364 Hydrogen bonds: A:Y.159, A:K.188, A:D.267, A:D.267, A:Y.305, A:N.366 Water bridges: A:N.268, A:N.268 Salt bridges: A:D.371 pi-Stacking: A:Y.159, A:Y.159 X1A.9: 22 residues within 4Å: Chain A: T.592, L.593, I.594 Chain B: G.157, F.158, Y.159, K.188, D.267, N.268, C.301, Y.305, T.336, V.340, V.341, W.364, N.366, V.369, D.371, Y.372, K.374, N.399, W.460 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.159, B:D.267, B:Y.305, B:W.364 Hydrogen bonds: B:Y.159, B:K.188, B:D.267, B:Y.305, B:N.366 Water bridges: B:N.268 Salt bridges: B:D.371 pi-Stacking: B:Y.159, B:Y.159

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.43, A.44, E.78, D.81 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.43, A:D.81, H2O.6, H2O.8, H2O.11

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: P.338, G.339, T.342 Chain B: N.480 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.338, A:T.342 Water bridges: A:G.308, A:T.342, A:N.343, A:N.343, A:N.343, A:W.460, B:N.480, B:N.480 SO4.4: 3 residues within 4Å: Chain A: R.523, S.570, F.571 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.571 Water bridges: A:R.523, A:S.570, A:A.572 SO4.5: 5 residues within 4Å: Chain A: N.285, K.290, D.328, P.329, S.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.285, A:S.330, A:S.330 Salt bridges: A:K.290 SO4.6: 2 residues within 4Å: Chain A: R.359, N.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.360, A:N.360, A:D.394 SO4.7: 4 residues within 4Å: Chain A: V.311, S.312, N.313, G.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.312, A:N.313, A:N.313 SO4.8: 3 residues within 4Å: Chain A: H.165, Q.166, R.208 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.166, A:R.208 Water bridges: A:Q.166, A:Q.166 Salt bridges: A:H.165 SO4.12: 3 residues within 4Å: Chain B: T.164, H.165, R.208 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.165 Water bridges: B:Q.166, B:R.208 Salt bridges: B:R.208 SO4.13: 4 residues within 4Å: Chain B: V.311, S.312, N.313, G.314 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.313 Water bridges: B:G.314 SO4.14: 3 residues within 4Å: Chain B: P.346, L.347, S.348 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.347, B:S.348, B:S.348, B:S.348 SO4.15: 5 residues within 4Å: Chain B: N.285, K.290, D.328, P.329, S.330 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.285, B:S.330, B:S.330 Salt bridges: B:K.290 SO4.16: 5 residues within 4Å: Chain B: R.234, F.235, D.236, A.239, K.276 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.235, B:D.236, B:D.236 Salt bridges: B:K.276

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

CL.10: 2 residues within 4Å: Chain B: R.359, N.360 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: P.514, E.515 Ligand excluded by PLIP

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

O-GlcNAcase NagJ: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

O-GlcNAcase NagJ

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