SMTL ID : 2gj4.1

Structure of rabbit muscle glycogen phosphorylase in complex with ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: W.56, Q.60, R.182, T.229 Chain B: V.29 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: H.190, W.204, R.340 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: Q.208, V.210, A.261, I.264, K.283 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: E.15, N.19, D.50, H.51 Chain B: F.26 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: L.538, Y.542, I.632, F.633, L.634, E.635 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: E.694, E.695, F.697, F.698, R.775 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: R.508, E.691, A.692, G.693, T.796 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: Q.397, L.400, N.401, A.404, L.414 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: V.29 Chain B: W.56, Q.60, R.182, T.229 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: H.190, W.204, R.340 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: Q.208, V.210, A.261, I.264, K.283 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: F.26 Chain B: E.15, N.19, D.50, H.51 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain B: L.538, Y.542, I.632, F.633, L.634, E.635 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: E.694, E.695, F.697, F.698, R.775 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain B: R.508, E.691, A.692, G.693, T.796 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain B: Q.397, L.400, N.401, A.404, L.414 Ligand excluded by PLIP

2 x PLR: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE(Covalent)

PLR.9: 14 residues within 4Å: Chain A: Y.79, G.123, G.124, W.480, V.556, K.557, K.563, Y.637, R.638, V.639, G.664, T.665, G.666, K.669 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.79, A:Y.637, A:K.669 Hydrogen bonds: A:T.665, A:T.665, A:G.666 Water bridges: A:Y.79, A:K.557, A:K.563, A:K.563, A:K.563, A:K.563, A:N.667, A:N.667 Salt bridges: A:K.557, A:K.563 PLR.19: 14 residues within 4Å: Chain B: Y.79, G.123, G.124, W.480, V.556, K.557, K.563, Y.637, R.638, V.639, G.664, T.665, G.666, K.669 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.79, B:Y.637, B:K.669 Hydrogen bonds: B:Y.637, B:T.665, B:T.665, B:G.666 Water bridges: B:K.557, B:K.563, B:K.563, B:K.563, B:K.563, B:N.667, B:N.667 Salt bridges: B:K.557, B:K.563

2 x 2TH: 2-CHLORO-N-[(1R,2R)-1-HYDROXY-2,3-DIHYDRO-1H-INDEN-2-YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE(Non-covalent)

2TH.10: 12 residues within 4Å: Chain A: R.49, W.56, P.177, E.179, K.180 Chain B: F.26, T.27, V.29, F.42, H.46, P.177 Ligands: 2TH.20 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.29, A:R.49, A:K.180 Hydrogen bonds: B:T.27, A:E.179 pi-Stacking: B:F.42, B:H.46 Water bridges: A:R.49, A:R.49, A:R.49 pi-Cation interactions: A:R.49 2TH.20: 12 residues within 4Å: Chain A: F.26, T.27, V.29, F.42, H.46, P.177 Chain B: R.49, W.56, P.177, E.179, K.180 Ligands: 2TH.10 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:R.49, B:K.180, A:V.29 Hydrogen bonds: B:E.179, A:T.27 Water bridges: B:R.49, B:R.49, B:R.49 pi-Cation interactions: B:R.49 pi-Stacking: A:F.42, A:H.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whittamore, P.R. et al., Novel thienopyrrole glycogen phosphorylase inhibitors: synthesis, in vitro SAR and crystallographic studies. Bioorg.Med.Chem.Lett. (2006)

Release Date

2007-02-13

Peptides

Glycogen phosphorylase, muscle form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycogen phosphorylase, muscle form