SMTL ID : 4cto.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 Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x M7C: N-[(2Z,5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-4-oxo-6-oxa-1-thia-3-azaspiro[4.5]dec-2-ylidene]benzamide(Non-covalent)

M7C.1: 18 residues within 4Å: Chain A: G.136, L.137, L.140, N.283, D.284, N.285, F.286, H.342, H.378, T.379, A.384, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.136, A:L.137, A:D.284, A:N.285, A:N.285, A:N.285, A:N.485, A:E.673, A:A.674, A:S.675, A:G.676 Water bridges: A:T.677 pi-Cation interactions: A:H.342 M7C.4: 18 residues within 4Å: Chain B: G.136, L.137, L.140, N.283, D.284, N.285, F.286, H.342, H.378, T.379, A.384, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.136, B:L.137, B:D.284, B:N.285, B:N.285, B:N.285, B:H.378, B:N.485, B:A.674, B:S.675, B:G.676 Water bridges: B:Y.574, B:Y.574, B:T.677 pi-Cation interactions: B:H.342

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

PLP.2: 15 residues within 4Å: Chain A: Y.91, 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 A Hydrophobic interactions: A:Y.91, A:Y.649, A:V.651, A:K.681 Hydrogen bonds: A:T.677, A:G.678 Water bridges: A:G.136, A:K.569, A:K.569, A:K.575, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.5: 15 residues within 4Å: Chain B: Y.91, 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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.91, 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:G.136, B:K.569, B:K.569, B:K.575, 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: F.197, R.243, R.310, R.311 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.243, A:R.310, A:R.311 PO4.6: 4 residues within 4Å: Chain B: F.197, R.243, R.310, R.311 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.243, B:R.310, B:R.311

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

Related Entries With Identical Sequence