SMTL ID : 3dyf.1

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461 and Isopentyl Diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.126, D.127, D.130, S.132 Ligands: NI9.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.4 MG.2: 3 residues within 4Å: Chain A: D.278, D.282 Ligands: NI9.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.278, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.126, D.130, Q.195, D.198 Ligands: NI9.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain B: D.126, D.130, S.132 Ligands: MG.10, NI9.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.126, B:D.130 MG.9: 2 residues within 4Å: Chain B: D.278 Ligands: NI9.11 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.278, H2O.9, H2O.11 MG.10: 5 residues within 4Å: Chain B: D.126, D.130, D.198 Ligands: MG.8, NI9.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, B:D.130, H2O.6

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: D.211 Chain B: P.139 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.144 Hydrogen bonds: A:D.211

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

NI9.5: 15 residues within 4Å: Chain A: Y.122, D.126, D.130, R.135, Q.195, K.235, T.236, Y.239, Q.275, D.278, K.292 Ligands: MG.1, MG.2, MG.3, IPR.6 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.235 Hydrogen bonds: A:D.126, A:D.126, A:D.126, A:R.135, A:R.135, A:K.235, A:Q.275, A:Q.275, A:Q.275 Water bridges: A:S.132, A:S.132, A:S.132, A:K.301, A:K.301, A:K.301 NI9.11: 14 residues within 4Å: Chain B: Y.122, D.126, D.130, R.135, Q.195, K.235, T.236, Q.275, D.278, K.292 Ligands: MG.8, MG.9, MG.10, IPR.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.235 Hydrogen bonds: B:R.135, B:R.135, B:K.235, B:Q.275 Water bridges: B:S.132, B:S.132

2 x IPR: ISOPENTYL PYROPHOSPHATE(Non-covalent)

IPR.6: 12 residues within 4Å: Chain A: G.69, K.70, R.73, Q.119, R.136, T.236, Y.239, T.240, F.274, Q.275, D.278 Ligands: NI9.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.236, A:F.274, A:D.278 Hydrogen bonds: A:K.70, A:Q.119, A:R.388 Water bridges: A:K.70, A:Y.71, A:N.72, A:R.73, A:K.292, A:K.292, A:K.292, A:K.292 Salt bridges: A:K.70, A:K.70, A:R.73, A:R.136, A:K.292 IPR.13: 13 residues within 4Å: Chain B: G.69, K.70, R.73, Q.119, R.136, T.236, Y.239, T.240, F.274, Q.275, D.278, R.388 Ligands: NI9.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.236, B:F.274, B:D.278 Hydrogen bonds: B:K.70, B:Q.119, B:R.388 Water bridges: B:Y.71, B:R.73, B:R.73 Salt bridges: B:K.70, B:K.70, B:R.73, B:R.73, B:R.136

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 5 residues within 4Å: Chain A: R.186, T.190, Y.238 Chain B: K.47, F.48 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.190, A:Y.238 Hydrogen bonds: A:R.186, A:R.186

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.12: 3 residues within 4Å: Chain B: C.182, R.183, R.186 No protein-ligand interaction detected (PLIP)

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

2009-05-05

Peptides

FARNESYL PYROPHOSPHATE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FARNESYL PYROPHOSPHATE SYNTHASE

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