SMTL ID : 5gn5.1 (1 other biounit)

Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with cumarin derivative-17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

2 x 6XZ: 4-[[4-(4-methoxyphenyl)piperazin-1-yl]methyl]-7,8-bis(oxidanyl)chromen-2-one(Non-covalent)

6XZ.1: 14 residues within 4Å: Chain A: R.86, E.87, P.137, S.139, Y.141, R.194, F.281, G.296, L.298, E.316, G.317, A.318, W.369 Ligands: GOL.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.298, A:W.369, A:W.369, A:W.369 Hydrogen bonds: A:R.86, A:E.87, A:R.194, A:E.316, A:A.318 pi-Stacking: A:Y.141 6XZ.3: 13 residues within 4Å: Chain B: R.86, E.87, K.116, S.139, Y.141, R.194, F.281, L.298, E.316, G.317, A.318, W.369 Ligands: GOL.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.141, B:W.369 Hydrogen bonds: B:R.86, B:E.87, B:S.139, B:R.194, B:A.318 pi-Stacking: B:Y.141

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Q.85, R.86, E.87, W.106, D.256, Q.257 Ligands: 6XZ.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.86, A:E.87, A:D.256, A:Q.257 GOL.4: 7 residues within 4Å: Chain B: R.86, E.87, W.106, D.256, Q.257, F.281 Ligands: 6XZ.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.86, B:R.86, B:R.86, B:E.87, B:Q.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balogun, E.O. et al., Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase ofTrypanosoma brucei brucei. Faseb J. (2019)

Release Date

2017-07-26

Peptides

Glycerol kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycerol kinase

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