SMTL ID : 4rxe.1

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x 3YQ: {[(3-methylpyridin-2-yl)amino]methanediyl}bis(phosphonic acid)(Non-covalent)

3YQ.1: 13 residues within 4Å: Chain A: Y.122, L.123, D.126, D.130, R.135, K.235, T.236, Y.239, D.278, K.292 Ligands: MG.2, MG.3, MG.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.123, A:D.126, A:Y.239 Hydrogen bonds: A:D.126, A:R.135, A:R.135, A:K.292, A:K.292 Water bridges: A:S.132, A:S.132, A:K.292 3YQ.5: 12 residues within 4Å: Chain B: L.123, D.126, D.130, R.135, K.235, T.236, Y.239, D.278, K.292 Ligands: MG.6, MG.7, MG.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.123, B:D.126, B:Y.239 Hydrogen bonds: B:D.130, B:R.135, B:R.135, B:K.292 Water bridges: B:S.132, B:S.132, B:Y.239

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.126, D.127, D.130, S.132, R.135 Ligands: 3YQ.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.3 MG.3: 3 residues within 4Å: Chain A: D.278, D.296 Ligands: 3YQ.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.278, H2O.2, H2O.3 MG.4: 5 residues within 4Å: Chain A: D.126, D.130, Q.195, D.198 Ligands: 3YQ.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, A:D.130, H2O.3 MG.6: 6 residues within 4Å: Chain B: D.126, D.127, D.130, S.132 Ligands: 3YQ.5, MG.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.7 MG.7: 4 residues within 4Å: Chain B: D.278, D.282, D.296 Ligands: 3YQ.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.278 MG.8: 5 residues within 4Å: Chain B: D.126, D.130, D.198 Ligands: 3YQ.5, MG.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.7

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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