SMTL ID : 4jvj.1

Crystal structure of human FPPS in complex with magnesium, CL01131, and sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x 1MV: ({[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)(Non-covalent)

1MV.1: 17 residues within 4Å: Chain A: F.121, D.125, M.128, D.129, R.134, T.189, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Chain B: N.152 Ligands: MG.3, MG.4, MG.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:D.125, A:T.189, A:Q.193, A:Q.193 Hydrogen bonds: A:D.125, A:D.129, A:R.134, A:R.134, A:K.222, A:K.222, A:Y.226, A:Q.262, A:D.265 Water bridges: A:D.269, A:K.288 pi-Cation interactions: A:K.222 1MV.6: 17 residues within 4Å: Chain A: N.152 Chain B: F.121, D.125, M.128, D.129, R.134, T.189, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.8, MG.9, MG.10 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:D.125, B:T.189, B:Q.193, B:Q.193 Hydrogen bonds: B:R.134, B:R.134, B:K.222, B:K.222, B:Q.262, B:D.265 Water bridges: B:K.288 pi-Cation interactions: B:K.222

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.79, A:Q.118 Water bridges: A:N.81, A:N.81, A:R.82, A:R.82 Salt bridges: A:R.82, A:R.135 SO4.7: 5 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.79, B:Q.118 Water bridges: B:N.81, B:N.81, B:R.82, B:R.82 Salt bridges: B:R.82, B:R.135

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: Q.262, D.265, D.266 Ligands: 1MV.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1 MG.4: 6 residues within 4Å: Chain A: D.125, D.129, D.196, K.288 Ligands: 1MV.1, MG.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.129, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: 1MV.1, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1 MG.8: 4 residues within 4Å: Chain B: Q.262, D.265, D.266 Ligands: 1MV.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.265, H2O.2, H2O.2 MG.9: 6 residues within 4Å: Chain B: D.125, D.129, D.196, K.288 Ligands: 1MV.6, MG.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.129, H2O.1, H2O.1 MG.10: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: 1MV.6, MG.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leung, C.Y. et al., Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition. J.Med.Chem. (2013)

Release Date

2014-01-01

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

Related Entries With Identical Sequence