SMTL ID : 6f3u.1

The crystal structure of Glycogen Phosphorylase in complex with 10h

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.649, A:V.651, A:K.681 Hydrogen bonds: A:T.677, A:G.678 Water bridges: A:G.136, A:K.569, A:K.569, A:K.575, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.4: 14 residues within 4Å: Chain B: 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.649, B:V.651, B:K.681 Hydrogen bonds: B:Y.649, B:T.677, B:G.678, B:K.681 Water bridges: B:G.136, B:K.569, B:K.569, B:K.575, B:N.679 Salt bridges: B:K.569, B:K.575

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.2: 6 residues within 4Å: Chain A: Q.73, Y.76, R.310, R.311 Chain B: D.43, V.46 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.310, A:R.311 pi-Stacking: A:Y.76, A:Y.76 Hydrogen bonds: B:D.43 IMP.5: 6 residues within 4Å: Chain A: D.43, V.46 Chain B: Q.73, Y.76, R.310, R.311 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.76, A:D.43 Salt bridges: B:R.310, B:R.311 pi-Stacking: B:Y.76, B:Y.76

2 x CNK: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(5-naphthalen-1-yl-4~{H}-1,2,4-triazol-3-yl)oxane-3,4,5-triol(Non-covalent)

CNK.3: 18 residues within 4Å: Chain A: E.89, G.136, L.137, L.140, N.283, N.285, F.286, H.342, H.378, A.384, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.137, A:A.384 Hydrogen bonds: A:N.285, A:N.485, A:E.673, A:E.673, A:A.674, A:S.675, A:G.676 Water bridges: A:L.137, A:T.677 pi-Cation interactions: A:H.342, A:H.342 CNK.6: 18 residues within 4Å: Chain B: E.89, G.136, L.137, L.140, N.283, N.285, F.286, H.342, H.378, A.384, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.137, B:A.384 Hydrogen bonds: B:N.285, B:H.378, B:N.485, B:Y.574, B:E.673, B:A.674, B:S.675, B:G.676 Water bridges: B:L.137, B:T.677 pi-Cation interactions: B:H.342, B:H.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kun, S. et al., A multidisciplinary study of 3-( beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors. Eur J Med Chem (2018)

Release Date

2018-02-28

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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