SMTL ID : 4dem.1

Crystal structure of human FPPS in complex with YS_04_70

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x YS4: [({4-[4-(propan-2-yloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)(Non-covalent)

YS4.1: 20 residues within 4Å: Chain A: F.121, A.124, D.125, M.128, 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.2, MG.3, MG.4 31 PLIP interactions: 2 interactions with chain B, 29 interactions with chain A Hydrophobic interactions: B:N.152, B:N.155, A:F.121, A:F.121, A:A.124, A:T.189, A:E.190, A:Q.193, A:Y.226 Hydrogen bonds: A:R.134, A:R.134, A:Q.262, A:K.279 Water bridges: A:D.125, A:D.129, A:D.129, A:S.131, A:S.131, A:S.131, A:D.196, A:K.222, A:K.222, A:K.222, A:K.222, A:Y.226, A:Y.226, A:Y.226, A:D.269, A:D.269, A:K.279, A:K.279 YS4.5: 20 residues within 4Å: Chain A: N.152, N.155 Chain B: F.121, A.124, D.125, M.128, D.129, R.134, T.189, E.190, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.6, MG.7, MG.8 28 PLIP interactions: 26 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.121, B:F.121, B:A.124, B:T.189, B:E.190, B:Q.193, B:Y.226, A:N.152, A:N.155 Hydrogen bonds: B:R.134, B:R.134, B:Q.262, B:K.279 Water bridges: B:D.125, B:S.131, B:S.131, B:S.131, B:S.131, B:D.196, B:K.222, B:K.222, B:K.222, B:K.222, B:T.223, B:Y.226, B:K.279, B:K.279, B:K.279

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.125, D.129, K.288 Ligands: YS4.1, 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.2 MG.3: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: YS4.1, MG.2 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: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: YS4.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain B: D.125, D.129, K.288 Ligands: YS4.5, MG.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.9, H2O.10, H2O.11 MG.7: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: YS4.5, MG.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.9, H2O.9 MG.8: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: YS4.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.9, H2O.9, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, Y.S. et al., Design and Synthesis of Active Site Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Apoptosis and Inhibition of ERK Phosphorylation in Multiple Myeloma Cells. J.Med.Chem. (2012)

Release Date

2012-03-21

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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