SMTL ID : 3dyg.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.126, D.130 Ligands: MG.3, 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.9 MG.2: 3 residues within 4Å: Chain A: D.278, K.292 Ligands: NI9.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.278, H2O.1, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.126, D.130, D.198 Ligands: MG.1, NI9.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: D.126, D.130 Ligands: MG.10, NI9.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.10, H2O.12 MG.9: 3 residues within 4Å: Chain B: Q.275, D.278 Ligands: NI9.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.278, B:D.278, H2O.10, H2O.10, H2O.17 MG.10: 5 residues within 4Å: Chain B: D.126, D.130, D.198 Ligands: MG.8, NI9.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.10, H2O.10, H2O.10

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

ACT.4: 5 residues within 4Å: Chain A: G.69, K.70, Q.119, R.136, K.390 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.136 Hydrogen bonds: A:K.70, A:Q.119 Water bridges: A:Y.71, A:Y.71, A:R.73, A:R.73, A:R.73, A:R.73, A:R.73 Salt bridges: A:R.73, A:R.136, A:K.390 ACT.11: 5 residues within 4Å: Chain B: G.69, K.70, R.73, Q.119, R.136 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.70 Water bridges: B:R.73, B:R.73, B:R.73 Salt bridges: B:K.70, B:R.136

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

NI9.5: 15 residues within 4Å: Chain A: Y.122, L.123, 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.239 Hydrogen bonds: A:D.126, A:D.126, A:R.135, A:R.135, A:Q.275, A:Q.275, A:K.292 Water bridges: A:S.132, A:S.132, A:S.132, A:S.132, A:K.235, A:K.235, A:Q.275 NI9.12: 14 residues within 4Å: Chain B: Y.122, D.126, D.130, R.135, Q.195, K.235, T.236, Y.239, Q.275, D.278, K.292 Ligands: MG.8, MG.9, MG.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.239 Hydrogen bonds: B:D.126, B:R.135, B:R.135, B:Q.275, B:Q.275 Water bridges: B:D.130, B:D.130, B:S.132, B:S.132, B:S.132, B:Q.195, B:K.235, B:K.235, B:D.282, B:D.282, B:D.282, B:K.292

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

BME.6: 4 residues within 4Å: Chain A: D.179, C.182, R.183, R.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.179 Water bridges: A:R.183 BME.13: 3 residues within 4Å: Chain B: C.182, R.183, R.186 No protein-ligand interaction detected (PLIP)

2 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, E.264 Chain B: K.47 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.186, A:T.190, A:Y.238 Hydrogen bonds: A:R.186 MPD.14: 5 residues within 4Å: Chain A: K.47, F.48 Chain B: R.186, T.190, Y.238 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.48

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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