SMTL ID : 3zct.1

Rabbit muscle glycogen phosphorylase b in complex with N-(2-naphthoyl) -N-beta-D-glucopyranosyl urea determined at 2.0 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.91, A:Y.649, A:V.651, A:K.681 Hydrogen bonds: A:Y.649, A:T.677, A:T.677, A:G.678 Water bridges: A:G.136, A:K.569, A:K.569, A:K.575, 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 17 PLIP interactions: 17 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:T.677, B:G.678, B:K.681 Water bridges: B:G.136, B:K.569, B:K.569, B:K.575, B:K.575, B:N.679 Salt bridges: B:K.569, B:K.575

4 x VMP: N-[[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]carbamoyl]naphthalene-2-carboxamide(Non-covalent)

VMP.2: 18 residues within 4Å: Chain A: R.61, V.65, W.68, P.189, W.190, E.191, K.192, A.193, P.230 Chain B: F.38, T.39, V.41, H.58, R.61, G.187, N.188, P.189 Ligands: VMP.6 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:R.61, A:V.65, A:W.68, A:K.192, A:K.192, A:P.230, B:V.41 Hydrogen bonds: A:R.61, B:T.39, B:R.61, B:R.61, B:N.188, B:N.188 Water bridges: A:E.191 pi-Cation interactions: A:R.61 VMP.4: 19 residues within 4Å: Chain A: E.89, N.134, G.136, L.137, L.140, N.283, D.284, F.287, H.342, H.378, A.384, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:D.284, A:A.384 Hydrogen bonds: A:G.136, A:L.137, A:N.485, A:N.485, A:Y.574, A:E.673, A:A.674, A:S.675, A:G.676 Water bridges: A:N.134, A:G.138, A:D.340, A:H.378, A:Y.574, A:T.677 VMP.6: 18 residues within 4Å: Chain A: F.38, T.39, V.41, H.58, R.61, G.187, N.188, P.189 Chain B: R.61, V.65, W.68, P.189, W.190, E.191, K.192, A.193, P.230 Ligands: VMP.2 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:R.61, B:V.65, B:W.68, B:K.192, B:K.192, B:P.230, A:V.41 Hydrogen bonds: B:R.61, A:T.39, A:R.61, A:R.61, A:N.188, A:N.188 Water bridges: B:E.191, A:E.191 pi-Cation interactions: B:R.61 VMP.8: 19 residues within 4Å: Chain B: E.89, N.134, G.136, L.137, L.140, N.283, D.284, F.287, H.342, H.378, A.384, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:D.284, B:A.384 Hydrogen bonds: B:G.136, B:L.137, B:H.378, B:N.485, B:N.485, B:A.674, B:S.675, B:G.676 Water bridges: B:N.134, B:G.138, B:D.284, B:D.340, B:H.378, B:Y.574, B:Y.574, B:Y.574, B:T.677

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 6 residues within 4Å: Chain A: Q.72, Q.73, Y.76, R.310, R.311 Chain B: V.46 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.82, A:R.82 Salt bridges: A:R.310, A:R.311 pi-Stacking: A:Y.76, A:Y.76 IMP.7: 6 residues within 4Å: Chain A: V.46 Chain B: Q.72, Q.73, Y.76, R.310, R.311 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.82, B:R.82 Salt bridges: B:R.310, B:R.311 pi-Stacking: B:Y.76, B:Y.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chrysina, E.D. et al., Synthesis, Kinetic, Computational and Crystallographic Evaluation of N-Acyl-N-Beta-D- Glucopyranosyl)Ureas, Nanomolar Glucose Analogue Inhibitors of Glycogen Phosphorylase, Potential Antidiabetic Agents. To be Published

Release Date

2013-12-11

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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