SMTL ID : 5diq.1

Crystal structure of human FPPS in complex with salicylic acid derivative 3a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: Y.137, R.138, K.141 Chain B: E.155, L.158, Q.159 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.138, A:R.138, A:Y.150 Water bridges: A:R.138, A:K.141 GOL.2: 6 residues within 4Å: Chain A: D.171, I.193, T.198, Q.237, D.241, C.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.171, A:D.241, A:C.264 GOL.6: 6 residues within 4Å: Chain A: E.155, L.158, Q.159 Chain B: Y.137, R.138, K.141 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.138, B:R.138, B:Y.150, B:Y.150 Water bridges: B:R.138, B:K.141 GOL.7: 6 residues within 4Å: Chain B: D.171, I.193, T.198, Q.237, D.241, C.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.171, B:D.241, B:C.264

2 x 5B9: 2-(naphthalen-1-ylmethoxy)benzoic acid(Non-covalent)

5B9.3: 13 residues within 4Å: Chain A: Y.7, K.54, N.56, R.57, T.60, S.202, F.203, F.236, K.254, L.341, K.344, I.345 Ligands: PO4.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.7, A:N.56, A:R.57, A:F.203, A:L.341, A:K.344, A:I.345 Hydrogen bonds: A:N.56 Water bridges: A:N.56, A:R.57, A:R.57 Salt bridges: A:K.54, A:R.57 pi-Stacking: A:F.236, A:F.236 pi-Cation interactions: A:K.54 5B9.8: 13 residues within 4Å: Chain B: Y.7, K.54, N.56, R.57, T.60, S.202, F.203, F.236, K.254, L.341, K.344, I.345 Ligands: PO4.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.7, B:N.56, B:R.57, B:F.203, B:L.341, B:K.344, B:I.345 Hydrogen bonds: B:N.56 Water bridges: B:N.56, B:R.57, B:R.57 Salt bridges: B:K.54, B:R.57 pi-Stacking: B:F.236, B:F.236 pi-Cation interactions: B:K.54

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: D.240 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.240, H2O.2, H2O.2, H2O.2, H2O.6, H2O.7 MG.9: 1 residues within 4Å: Chain B: D.240 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.240, H2O.9, H2O.10, H2O.10, H2O.14, H2O.14

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

PO4.5: 5 residues within 4Å: Chain A: G.53, K.54, Q.93, R.110 Ligands: 5B9.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.54 Water bridges: A:Y.55, A:R.57, A:R.57, A:Q.93, A:Q.93, A:Q.93, A:R.110 Salt bridges: A:R.110 PO4.10: 5 residues within 4Å: Chain B: G.53, K.54, Q.93, R.110 Ligands: 5B9.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.54 Water bridges: B:Y.55, B:R.57, B:R.57, B:Q.93, B:Q.93, B:Q.93, B:R.110 Salt bridges: B:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marzinzik, A.L. et al., Discovery of Novel Allosteric Non-Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthase by Integrated Lead Finding. Chemmedchem (2015)

Release Date

2015-09-30

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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