SMTL ID : 4ctm.1

Glucopyranosylidene-spiro-iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetic and Crystallographic Methods

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x MIF: (5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-2-imino-6-oxa-1-thia-3-azaspiro[4.5]decan-4-one(Non-covalent)

MIF.1: 12 residues within 4Å: Chain A: G.136, L.137, L.140, N.285, H.378, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.136, A:L.137, A:N.285, A:N.285, A:N.485, A:E.673, A:E.673, A:E.673, A:A.674, A:S.675, A:G.676, A:G.676 Water bridges: A:D.284, A:D.284, A:D.284, A:T.677 MIF.4: 12 residues within 4Å: Chain B: G.136, L.137, L.140, N.285, H.378, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.136, B:L.137, B:N.285, B:N.285, B:H.378, B:N.485, B:E.673, B:E.673, B:A.674, B:S.675, B:G.676, B:G.676 Water bridges: B:D.284, B:D.284, B:D.284, B:Y.574, B:Y.574, B:T.677

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.2: 14 residues within 4Å: Chain A: G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.649, A:V.651, A:K.681 Hydrogen bonds: A:T.677, A:G.678 Water bridges: A:K.569, A:K.575, A:N.679, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.5: 14 residues within 4Å: Chain B: G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.649, B:V.651, B:K.681 Hydrogen bonds: B:Y.649, B:T.677, B:G.678, B:K.681 Water bridges: B:K.569, B:K.575, B:N.679, B:N.679 Salt bridges: B:K.569, B:K.575

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: H.202, W.216, R.352, L.357 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.352, A:R.352 Salt bridges: A:H.202, A:R.352 PO4.6: 4 residues within 4Å: Chain B: H.202, W.216, R.352, L.357 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.352, B:R.352 Salt bridges: B:H.202, B:R.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czifrak, K. et al., Glucopyranosylidene-Spiro-Iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation for Inhibition of Glycogen Phosphorylase by Enzyme Kinetic and Crystallographic Methods. Bioorg.Med.Chem. (2014)

Release Date

2014-08-06

Peptides

GLYCOGEN PHOSPHORYLASE, MUSCLE FORM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLYCOGEN PHOSPHORYLASE, MUSCLE FORM

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