SMTL ID : 3ddw.1

Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK055

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NBG: N-acetyl-beta-D-glucopyranosylamine(Non-covalent)

NBG.1: 13 residues within 4Å: Chain A: G.137, L.138, N.286, D.341, H.379, T.380, V.457, N.486, Y.575, E.674, A.675, S.676, G.677 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:H.379, A:T.380 Hydrogen bonds: A:N.286, A:N.286, A:H.379, A:H.379, A:N.486, A:N.486, A:E.674, A:E.674, A:A.675, A:S.676, A:G.677, A:G.677 Water bridges: A:L.138, A:N.286, A:K.576, A:K.576, A:K.576, A:T.678 NBG.6: 13 residues within 4Å: Chain B: G.137, L.138, N.286, D.341, H.379, T.380, V.457, N.486, Y.575, E.674, A.675, S.676, G.677 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.138, B:H.379, B:T.380 Hydrogen bonds: B:N.286, B:N.286, B:H.379, B:N.486, B:N.486, B:E.674, B:A.675, B:S.676, B:G.677, B:G.677 Water bridges: B:L.138, B:N.286, B:K.576, B:K.576, B:T.678

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

PLP.2: 15 residues within 4Å: Chain A: Y.92, G.136, G.137, W.493, V.569, K.570, K.576, Y.650, R.651, V.652, A.655, G.677, T.678, G.679, K.682 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.92, A:Y.650, A:V.652, A:K.682 Hydrogen bonds: A:T.678, A:G.679 Water bridges: A:G.137, A:K.570, A:K.570, A:K.576, A:K.576, A:N.680 Salt bridges: A:K.570, A:K.576 PLP.7: 14 residues within 4Å: Chain B: Y.92, G.136, G.137, W.493, K.570, K.576, Y.650, R.651, V.652, A.655, G.677, T.678, G.679, K.682 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.92, B:Y.650, B:V.652, B:K.682 Hydrogen bonds: B:Y.650, B:T.678, B:T.678, B:G.679 Water bridges: B:Y.92, B:G.137, B:K.570, B:K.570, B:K.576, B:N.680 Salt bridges: B:K.570, B:K.576

2 x CFF: CAFFEINE(Non-covalent)

CFF.3: 6 residues within 4Å: Chain A: N.284, F.287, H.573, A.612, G.614, Y.615 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.772 pi-Stacking: A:F.287, A:F.287, A:Y.615 CFF.8: 6 residues within 4Å: Chain B: N.284, F.287, H.573, A.612, G.614, Y.615 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.772 pi-Stacking: B:F.287, B:F.287, B:Y.615

2 x 055: (2S)-{[(3-{[(2-chloro-6-methylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]amino}(phenyl)ethanoic acid(Non-covalent)

055.4: 13 residues within 4Å: Chain A: W.69, I.70, Q.73, Q.74, R.195, F.198, D.229, R.244, R.312 Chain B: V.42, K.43, D.44, V.47 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.69, A:I.70, A:Q.73, A:Q.73, A:Q.74, A:Q.74, B:V.42, B:V.47 Hydrogen bonds: A:Q.73, B:V.42, B:D.44 Water bridges: A:R.83, A:R.312 Salt bridges: A:R.83, A:R.312 pi-Stacking: A:W.69, A:F.198 pi-Cation interactions: A:R.195 055.11: 16 residues within 4Å: Chain A: V.42, K.43, D.44, N.46, V.47 Chain B: W.69, I.70, Q.73, Q.74, Y.77, R.195, F.198, D.229, R.244, R.311, R.312 22 PLIP interactions: 5 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:V.42, A:V.47, A:V.47, B:W.69, B:I.70, B:Q.73, B:Q.73, B:Q.74, B:Q.74, B:Y.77, B:R.311 Hydrogen bonds: A:V.42, A:D.44, B:Q.73, B:R.195 Water bridges: B:R.83, B:R.83 Salt bridges: B:R.83, B:R.312 pi-Stacking: B:W.69, B:F.198 pi-Cation interactions: B:R.195

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 3 residues within 4Å: Chain A: H.203, W.217, R.353 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.353 MPD.12: 5 residues within 4Å: Chain B: L.495, E.503, A.506, E.511, Y.513 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.495, B:E.503 Hydrogen bonds: B:E.511, B:E.511

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.9: 8 residues within 4Å: Chain B: I.172, R.173, D.174, G.175, E.554, Y.555, T.626, E.648 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.175 Water bridges: B:D.174 Salt bridges: B:E.648 MES.10: 7 residues within 4Å: Chain B: R.51, R.95, E.126, I.127, E.128, E.129, R.651 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.95, B:R.651 Water bridges: B:R.51, B:D.130 Salt bridges: B:R.51, B:E.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomson, S.A. et al., Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy. Bioorg.Med.Chem.Lett. (2009)

Release Date

2009-01-27

Peptides

Glycogen phosphorylase, liver form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycogen phosphorylase, liver form

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