SMTL ID : 4l2x.1

Crystal structure of human FPPS in complex with magnesium, CL02134, and inorganic pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x YL2: ({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)(Non-covalent)

YL2.1: 19 residues within 4Å: Chain A: F.120, F.121, D.125, D.129, R.134, T.189, E.190, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Chain B: N.152, N.155 Ligands: MG.3, MG.4, MG.5 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.120, A:F.121, A:F.121, A:T.189, A:E.190, A:Q.193, A:Q.193 Hydrogen bonds: A:D.125, A:D.125, A:R.134, A:R.134, A:K.222, A:Y.226, A:Q.262 Water bridges: A:S.131, A:S.131, A:Q.193, A:K.222, A:K.222, A:K.222, A:K.222, A:D.269, A:D.269, A:K.279 pi-Cation interactions: A:K.222 YL2.6: 19 residues within 4Å: Chain A: N.152, N.155 Chain B: F.120, F.121, D.125, D.129, R.134, T.189, E.190, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.8, MG.9, MG.10 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:F.120, B:F.121, B:F.121, B:T.189, B:E.190, B:Q.193, B:Q.193 Hydrogen bonds: B:D.125, B:D.125, B:R.134, B:R.134, B:K.222, B:Q.262 Water bridges: B:S.131, B:S.131, B:Q.193, B:K.222, B:K.222, B:K.222, B:K.222, B:K.279 pi-Cation interactions: B:K.222

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 6 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135, F.261 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.79, A:R.82, A:Q.118 Water bridges: A:G.78, A:Y.80, A:N.81, A:N.81, A:E.115 Salt bridges: A:K.79, A:K.79, A:R.82, A:R.135, A:K.279 POP.7: 6 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135, F.261 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.79, B:R.82, B:Q.118 Water bridges: B:G.78, B:Y.80, B:N.81, B:N.81, B:E.115 Salt bridges: B:K.79, B:K.79, B:R.82, B:R.135, B:K.279

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: YL2.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.1 MG.4: 6 residues within 4Å: Chain A: D.125, D.129, D.196, K.288 Ligands: YL2.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.1, H2O.1 MG.5: 2 residues within 4Å: Chain A: D.265 Ligands: YL2.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: YL2.6, MG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.1, H2O.1 MG.9: 6 residues within 4Å: Chain B: D.125, D.129, D.196, K.288 Ligands: YL2.6, MG.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.1, H2O.1, H2O.1 MG.10: 2 residues within 4Å: Chain B: D.265 Ligands: YL2.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.1, H2O.1, 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

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