SMTL ID : 2opm.1

Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: G.77, K.78, Y.79, R.81, Q.117, R.134 Ligands: PO4.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.78, A:Y.79, A:Q.117 Water bridges: A:G.77, A:K.78, A:R.81, A:E.114 Salt bridges: A:K.78, A:R.81, A:R.134 PO4.2: 5 residues within 4Å: Chain A: K.78, R.81, Q.117, F.260 Ligands: PO4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.117 Water bridges: A:K.78 Salt bridges: A:K.78, A:R.81, A:K.278 PO4.7: 7 residues within 4Å: Chain B: G.77, K.78, Y.79, R.81, Q.117, R.134 Ligands: PO4.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.78, B:Y.79, B:Q.117 Water bridges: B:K.78, B:R.81, B:E.114, B:E.114 Salt bridges: B:K.78, B:R.81, B:R.134 PO4.8: 5 residues within 4Å: Chain B: K.78, R.81, Q.117, F.260 Ligands: PO4.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.117 Water bridges: B:K.78 Salt bridges: B:K.78, B:R.81, B:K.278

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.124, D.128 Ligands: MG.5, NI9.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.124, A:D.128, H2O.2, H2O.4 MG.4: 2 residues within 4Å: Chain A: D.264 Ligands: NI9.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.264, H2O.3 MG.5: 7 residues within 4Å: Chain A: D.124, D.128, Q.192, D.195, K.287 Ligands: MG.3, NI9.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.124, A:D.128, H2O.3 MG.9: 4 residues within 4Å: Chain B: D.124, D.128 Ligands: MG.11, NI9.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.124, B:D.128, H2O.7, H2O.9 MG.10: 2 residues within 4Å: Chain B: D.264 Ligands: NI9.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.264, H2O.8 MG.11: 7 residues within 4Å: Chain B: D.124, D.128, Q.192, D.195, K.287 Ligands: MG.9, NI9.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.124, B:D.128, H2O.8

2 x NI9: 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM(Non-covalent)

NI9.6: 13 residues within 4Å: Chain A: D.124, D.128, R.133, T.188, Q.192, K.221, T.222, Q.261, D.264, K.278 Ligands: MG.3, MG.4, MG.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.188, A:K.221 Hydrogen bonds: A:D.124, A:R.133, A:R.133, A:K.221, A:K.221, A:Q.261, A:Q.261, A:K.278 Water bridges: A:D.124, A:D.124 NI9.12: 13 residues within 4Å: Chain B: D.124, D.128, R.133, T.188, Q.192, K.221, T.222, Q.261, D.264, K.278 Ligands: MG.9, MG.10, MG.11 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.188, B:K.221 Hydrogen bonds: B:D.124, B:R.133, B:R.133, B:K.221, B:K.221, B:Q.261, B:Q.261, B:K.278 Water bridges: B:D.124, B:D.124, B:D.128, B:D.128, B:D.128, B:D.195, B:D.265, B:D.268, B:D.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation. J.Am.Chem.Soc. (2009)

Release Date

2007-12-11

Peptides

Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltranstransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.10)]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltranstransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.10)]

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