SMTL ID : 5djr.1

Crystal structure of human FPPS in complex with biaryl compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Y.137, R.138, K.141, Y.150 Chain B: E.155, L.158, Q.159 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.150, B:E.155 Water bridges: A:R.138, B:L.158 GOL.2: 4 residues within 4Å: Chain A: Y.116, Q.117, K.118, G.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.118, A:G.122 GOL.5: 7 residues within 4Å: Chain A: E.155, L.158, Q.159 Chain B: Y.137, R.138, K.141, Y.150 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.138, B:Y.150, A:L.158 GOL.6: 4 residues within 4Å: Chain B: Y.116, Q.117, K.118, G.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.118, B:G.122

2 x 5BK: 1H,1'H-4,4'-biindole-2-carboxylic acid(Non-covalent)

5BK.3: 11 residues within 4Å: Chain A: Y.7, K.54, N.56, R.57, T.60, S.202, F.203, F.236, L.341, K.344 Ligands: PO4.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:N.56, A:R.57, A:F.203, A:F.203, A:F.236, A:F.236 Hydrogen bonds: A:Y.7, A:K.54, A:N.56, A:R.57, A:T.60 Water bridges: A:K.54, A:K.54 Salt bridges: A:K.54 pi-Stacking: A:F.236 5BK.7: 11 residues within 4Å: Chain B: Y.7, K.54, N.56, R.57, T.60, S.202, F.203, F.236, L.341, K.344 Ligands: PO4.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:N.56, B:R.57, B:F.203, B:F.203, B:F.236, B:F.236 Hydrogen bonds: B:K.54, B:N.56, B:R.57, B:T.60, B:T.60 Water bridges: B:K.54, B:K.54 Salt bridges: B:K.54 pi-Stacking: B:F.236

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

PO4.4: 5 residues within 4Å: Chain A: G.53, K.54, Q.93, R.110 Ligands: 5BK.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.54, A:R.57, A:Q.93, A:Q.93 Water bridges: A:Y.55, A:Y.55 Salt bridges: A:R.110 PO4.8: 5 residues within 4Å: Chain B: G.53, K.54, Q.93, R.110 Ligands: 5BK.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.54, B:R.57, B:Q.93, B:Q.93 Water bridges: B:Y.55, B:Y.55 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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