SMTL ID : 4rxc.1

T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate BPH-6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

4 x HRX: [1-hydroxy-3-(pyridin-3-yl)propane-1,1-diyl]bis(phosphonic acid)(Non-covalent)

HRX.1: 12 residues within 4Å: Chain A: Y.122, D.126, D.130, R.135, T.191, Q.195, K.235, Y.239 Ligands: MG.2, MG.3, MG.4, HRX.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.122, A:Q.195 Hydrogen bonds: A:R.135, A:R.135, A:D.198, A:K.235 HRX.5: 8 residues within 4Å: Chain A: F.274, Q.275, D.278, K.292, R.388 Ligands: HRX.1, MG.4, MG.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.274 Hydrogen bonds: A:Q.275, A:K.292, A:K.292 Water bridges: A:K.235 pi-Stacking: A:F.274 HRX.7: 14 residues within 4Å: Chain B: Y.122, L.123, D.126, D.130, R.135, T.191, Q.195, K.235, Y.239, K.301 Ligands: MG.8, MG.9, MG.10, HRX.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Q.195 Hydrogen bonds: B:D.126, B:D.130, B:R.135, B:R.135, B:Y.239 Water bridges: B:D.130, B:S.132, B:D.198 HRX.11: 7 residues within 4Å: Chain B: F.274, Q.275, D.278, K.292 Ligands: HRX.7, MG.10, MG.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.275, B:K.292, B:K.292 pi-Stacking: B:F.274

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: D.126, D.130 Ligands: HRX.1, MG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.126, A:D.130 MG.3: 4 residues within 4Å: Chain A: D.126, D.130 Ligands: HRX.1, MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.126, A:D.130 MG.4: 2 residues within 4Å: Ligands: HRX.1, HRX.5 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: D.278, K.292, D.296 Ligands: HRX.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.278 MG.8: 4 residues within 4Å: Chain B: D.126, D.130 Ligands: HRX.7, MG.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.6 MG.9: 4 residues within 4Å: Chain B: D.126, D.130 Ligands: HRX.7, MG.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.6 MG.10: 2 residues within 4Å: Ligands: HRX.7, HRX.11 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain B: D.278, K.292, D.296 Ligands: HRX.11 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.278, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y.L. et al., Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries. ACS Med Chem Lett (2015)

Release Date

2015-04-15

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl pyrophosphate synthase

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