SMTL ID : 4qxs.1

Crystal structure of human FPPS in complex with WC01088

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: G.78, K.79, Q.118, R.135 Ligands: PO4.2, WC1.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.79, A:Q.118 Water bridges: A:Y.80, A:R.82, A:R.82, A:R.82 Salt bridges: A:K.79, A:R.135 PO4.2: 3 residues within 4Å: Chain A: R.134, R.135 Ligands: PO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.135, A:R.135 Salt bridges: A:K.79, A:R.134 PO4.5: 6 residues within 4Å: Chain B: G.78, K.79, Q.118, R.135 Ligands: PO4.6, WC1.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.79, B:Q.118 Water bridges: B:Y.80, B:R.82, B:R.82 Salt bridges: B:K.79, B:R.135 PO4.6: 3 residues within 4Å: Chain B: R.134, R.135 Ligands: PO4.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.135, B:R.135 Salt bridges: B:K.79, B:R.134

2 x WC1: (2-{2-[(2S)-3-methylbutan-2-yl]-5-phenyl-1H-indol-3-yl}ethane-1,1-diyl)bis(phosphonic acid)(Non-covalent)

WC1.3: 14 residues within 4Å: Chain A: K.79, N.81, R.82, T.85, S.227, F.228, F.261, D.265, L.268, V.276, L.366, K.369, I.370 Ligands: PO4.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:K.79, A:N.81, A:R.82, A:L.268, A:L.366, A:I.370 Hydrogen bonds: A:K.79, A:N.81, A:R.82, A:R.82, A:D.265 Water bridges: A:K.79, A:K.79, A:Q.118, A:Q.118, A:Q.264, A:K.369 pi-Stacking: A:F.228, A:F.261 pi-Cation interactions: A:K.369 WC1.7: 14 residues within 4Å: Chain B: K.79, N.81, R.82, T.85, S.227, F.228, F.261, D.265, L.268, V.276, L.366, K.369, I.370 Ligands: PO4.5 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:K.79, B:N.81, B:R.82, B:L.268, B:L.366, B:I.370 Hydrogen bonds: B:K.79, B:N.81, B:R.82, B:R.82, B:D.265 Water bridges: B:K.79, B:K.79, B:Q.118, B:Q.118, B:Q.264, B:K.369 pi-Stacking: B:F.228, B:F.261 pi-Cation interactions: B:K.369

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Y.162, R.163, K.166, Y.175 Chain B: E.180, L.183, Q.184 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.163 Hydrogen bonds: B:L.183 GOL.8: 7 residues within 4Å: Chain A: E.180, L.183, Q.184 Chain B: Y.162, R.163, K.166, Y.175 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.175, A:L.183 Water bridges: B:R.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gritzalis, D. et al., Probing the molecular and structural elements of ligands binding to the active site versus an allosteric pocket of the human farnesyl pyrophosphate synthase. Bioorg.Med.Chem.Lett. (2015)

Release Date

2015-02-25

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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