SMTL ID : 2qn9.1

Glycogen Phosphorylase in complex with N-4-aminobenzoyl-N'-beta-D-glucopyranosyl urea

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.90, G.134, G.135, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.648, A:V.650, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:G.677 Water bridges: A:G.135, A:K.574, A:K.574, A:N.678, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.4: 15 residues within 4Å: Chain B: Y.90, G.134, G.135, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.90, B:Y.648, B:V.650, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:T.676, B:G.677 Water bridges: B:G.135, B:K.574, B:K.574, B:N.678, B:N.678 Salt bridges: B:K.568, B:K.574

2 x NBX: N-{[(4-aminophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine(Non-covalent)

NBX.2: 16 residues within 4Å: Chain A: E.88, N.133, G.135, L.136, L.139, N.282, D.283, R.292, H.341, H.377, N.484, Y.573, E.672, A.673, S.674, G.675 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:D.283 Hydrogen bonds: A:L.136, A:Y.573, A:E.672, A:E.672, A:S.674, A:S.674, A:G.675 Water bridges: A:G.135, A:G.137, A:N.282, A:N.282, A:D.283, A:R.292, A:R.292, A:H.377, A:A.673, A:T.676 pi-Cation interactions: A:H.341 NBX.5: 16 residues within 4Å: Chain B: E.88, N.133, G.135, L.136, L.139, N.282, D.283, R.292, H.341, H.377, N.484, Y.573, E.672, A.673, S.674, G.675 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:D.283 Hydrogen bonds: B:L.136, B:H.377, B:E.672, B:S.674, B:S.674, B:G.675 Water bridges: B:G.135, B:G.137, B:N.282, B:N.282, B:D.283, B:D.283, B:R.292, B:R.292, B:H.377, B:Y.573, B:Y.573, B:A.673, B:T.676 pi-Cation interactions: B:H.341

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 7 residues within 4Å: Chain A: Q.71, Q.72, Y.75, R.309, R.310 Chain B: D.42, V.45 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Water bridges: A:R.81, A:R.242 Salt bridges: A:R.309, A:R.310 pi-Stacking: A:Y.75, A:Y.75 Hydrogen bonds: B:D.42 IMP.6: 7 residues within 4Å: Chain A: D.42, V.45 Chain B: Q.71, Q.72, Y.75, R.309, R.310 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.75, A:D.42 Water bridges: B:Y.155, B:R.242 Salt bridges: B:R.309, B:R.310 pi-Stacking: B:Y.75, B:Y.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagy, V. et al., N-(4-substituted-benzoyl)-N'-(beta-D-glucopyranosyl)ureas, inhibitors of glycogen phosphorylase: synthesis, kinetic and crystallographic evaluation. To be Published

Release Date

2008-07-22

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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