SMTL ID : 4mhs.1

Crystal structure of Gpb in complex with SUGAR (N-[(2E)-3-(BIPHENYL-4-YL)PROP-2-ENOYL]-BETA-D-GLUCOPYRANOSYLAMINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 26Q: N-[(2E)-3-(biphenyl-4-yl)prop-2-enoyl]-beta-D-glucopyranosylamine(Non-covalent)

26Q.1: 20 residues within 4Å: Chain A: E.77, N.122, G.124, L.125, L.128, N.271, D.272, F.275, R.281, H.330, H.366, E.374, V.444, N.473, Y.562, E.661, A.662, S.663, G.664, T.665 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.125, A:D.272, A:F.275, A:R.281 Hydrogen bonds: A:G.124, A:L.125, A:H.366, A:N.473, A:E.661, A:A.662, A:S.663, A:G.664 Water bridges: A:G.126, A:T.665 pi-Cation interactions: A:R.281, A:H.330 26Q.3: 20 residues within 4Å: Chain B: E.77, N.122, G.124, L.125, L.128, N.271, D.272, F.275, R.281, H.330, H.366, E.374, V.444, N.473, Y.562, E.661, A.662, S.663, G.664, T.665 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.125, B:D.272, B:F.275, B:R.281 Hydrogen bonds: B:G.124, B:L.125, B:H.366, B:H.366, B:N.473, B:Y.562, B:A.662, B:S.663, B:G.664 Water bridges: B:G.126, B:D.272, B:T.665 pi-Cation interactions: B:R.281, B:H.330

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 6 residues within 4Å: Chain A: R.82, T.83, L.84, Q.85, E.112, E.115 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.84, A:Q.85 Water bridges: A:R.479 Salt bridges: A:E.112, A:E.115 DMS.4: 6 residues within 4Å: Chain B: R.82, T.83, L.84, Q.85, E.112, E.115 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.84, B:Q.85 Water bridges: B:R.479 Salt bridges: B:E.112, B:E.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parmenopoulou, V. et al., Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-beta-d-glucopyranosylamines. Bioorg.Med.Chem. (2014)

Release Date

2014-07-23

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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