SMTL ID : 9frm.1

The crystal structure of glycogen phosphorylase with an indole derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 01: (7~{S})-1-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)amino]-6,6-dimethyl-7-oxidanyl-7,8-dihydrobenzo[cd]indole-3-carboxylic acid

01.1: 14 residues within 4Å: Chain A: N.31, R.34, H.35, F.38, T.39, D.62 Chain B: E.27, N.31, R.34, H.35, F.38, T.39, D.62 Ligands: 01.19 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.31, B:T.39 Water bridges: B:R.61, A:D.62 Salt bridges: B:R.34, A:R.34 Hydrophobic interactions: A:F.38 pi-Cation interactions: A:R.34 01.19: 14 residues within 4Å: Chain A: E.27, N.31, R.34, H.35, F.38, T.39, D.62 Chain B: N.31, R.34, H.35, F.38, T.39, D.62 Ligands: 01.1 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.31 Water bridges: A:R.61 Salt bridges: A:R.34, B:R.34 Hydrophobic interactions: B:F.38 pi-Cation interactions: B:R.34

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

DMS.2: 7 residues within 4Å: Chain A: R.67, N.102, L.103, A.104, R.235, N.237, R.834 Ligand excluded by PLIP DMS.3: 7 residues within 4Å: Chain A: L.550, Y.554, V.556, I.644, F.645, L.646, E.647 Ligand excluded by PLIP DMS.4: 6 residues within 4Å: Chain A: R.520, E.702, E.703, A.704, G.705 Ligands: DMS.13 Ligand excluded by PLIP DMS.5: 5 residues within 4Å: Chain A: E.707, F.709, F.710, R.787, M.801 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: D.723, Q.724, R.725, G.726 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: Y.727, H.768, H.769, D.770 Ligand excluded by PLIP DMS.8: 4 residues within 4Å: Chain A: Q.409, L.412, N.413, A.416 Ligand excluded by PLIP DMS.9: 9 residues within 4Å: Chain A: Q.265, L.268, D.269, N.271, L.272 Chain B: N.271, L.272, N.275 Ligands: DMS.27 Ligand excluded by PLIP DMS.10: 4 residues within 4Å: Chain A: F.197, R.243, R.310, R.311 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain A: H.202, W.216, R.352, L.357 Ligand excluded by PLIP DMS.12: 8 residues within 4Å: Chain A: F.203, Q.220, V.222, L.272, A.273, I.276, K.295 Ligands: DMS.15 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: R.520, E.702, E.703 Ligands: DMS.4 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: W.68, I.69, Q.72, R.194 Chain B: V.41 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: L.272, N.275, K.295 Ligands: DMS.12 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain A: I.264 Chain B: Y.281, K.290 Ligand excluded by PLIP DMS.17: 3 residues within 4Å: Chain A: S.524, Y.525, D.528 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: A.505, E.506, R.507, I.508, G.509 Ligand excluded by PLIP DMS.20: 7 residues within 4Å: Chain B: R.67, N.102, L.103, A.104, R.235, N.237, R.834 Ligand excluded by PLIP DMS.21: 7 residues within 4Å: Chain B: L.550, Y.554, V.556, I.644, F.645, L.646, E.647 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain B: R.520, E.702, E.703, A.704, G.705 Ligands: DMS.31 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain B: E.707, F.709, F.710, R.787, M.801 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain B: D.723, Q.724, R.725, G.726 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain B: Y.727, H.768, H.769, D.770 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain B: Q.409, L.412, N.413, A.416 Ligand excluded by PLIP DMS.27: 9 residues within 4Å: Chain A: N.271, L.272, N.275 Chain B: Q.265, L.268, D.269, N.271, L.272 Ligands: DMS.9 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain B: F.197, R.243, R.310, R.311 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain B: H.202, W.216, R.352, L.357 Ligand excluded by PLIP DMS.30: 8 residues within 4Å: Chain B: F.203, Q.220, V.222, L.272, A.273, I.276, K.295 Ligands: DMS.33 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain B: R.520, E.702, E.703 Ligands: DMS.22 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain A: V.41 Chain B: W.68, I.69, Q.72, R.194 Ligand excluded by PLIP DMS.33: 4 residues within 4Å: Chain B: L.272, N.275, K.295 Ligands: DMS.30 Ligand excluded by PLIP DMS.34: 3 residues within 4Å: Chain A: Y.281, K.290 Chain B: I.264 Ligand excluded by PLIP DMS.35: 3 residues within 4Å: Chain B: S.524, Y.525, D.528 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: A.505, E.506, R.507, I.508, G.509 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arunrattiyakorn, P. et al., Synthesis and evaluation of tetrahydrobenzo[cd]indole derivatives as glycogen phosphorylase inhibitors. Med.Chem.Res. (2025)

Release Date

2025-05-07

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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