SMTL ID : 5jv0.1

Crystal structure of human FPPS in complex with an allosteric inhibitor CL-08-038

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: H.57, P.58, E.59, I.60 Chain B: S.217, K.220, Y.221 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.57, A:E.59, A:I.60, B:Y.221 Salt bridges: A:H.57, B:K.220 SO4.2: 6 residues within 4Å: Chain A: G.78, K.79, Y.80, N.81, R.82 Ligands: YL5.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.79, A:Y.80, A:N.81, A:N.81 Water bridges: A:R.82, A:R.82 Salt bridges: A:R.82 SO4.6: 7 residues within 4Å: Chain A: S.217, K.220, Y.221 Chain B: H.57, P.58, E.59, I.60 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.57, B:E.59, B:I.60 Salt bridges: B:H.57, A:K.220 SO4.7: 6 residues within 4Å: Chain B: G.78, K.79, Y.80, N.81, R.82 Ligands: YL5.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.79, B:Y.80, B:N.81, B:N.81 Water bridges: B:R.82, B:R.82 Salt bridges: B:R.82

6 x YL5: [(1R)-2-(3-fluorophenyl)-1-{[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}ethyl]phosphonic acid(Non-covalent)

YL5.3: 13 residues within 4Å: Chain A: N.81, R.82, T.85, S.227, F.228, F.261, Q.264, L.268, T.277, L.366, K.369, K.372 Ligands: SO4.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.81, A:R.82, A:F.228, A:F.228, A:L.268 Hydrogen bonds: A:K.369, A:K.369, A:K.369 Water bridges: A:N.81, A:N.81 YL5.4: 12 residues within 4Å: Chain A: R.91, E.92, L.93, V.94, E.95, P.96, K.98, A.239, I.241, P.357, L.358, P.359 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.95, A:P.96, A:I.241, A:I.241 Hydrogen bonds: A:L.93, A:L.93, A:E.95, A:E.95 YL5.5: 8 residues within 4Å: Chain A: E.340, E.341, Y.344, M.348, L.364, R.368, Y.371, K.372 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.341, A:Y.344, A:R.368, A:Y.371 Hydrogen bonds: A:Y.371 YL5.8: 13 residues within 4Å: Chain B: N.81, R.82, T.85, S.227, F.228, F.261, Q.264, L.268, T.277, L.366, K.369, K.372 Ligands: SO4.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:N.81, B:R.82, B:F.228, B:F.228, B:L.268 Hydrogen bonds: B:K.369, B:K.369, B:K.369 Water bridges: B:N.81, B:N.81 YL5.9: 12 residues within 4Å: Chain B: R.91, E.92, L.93, V.94, E.95, P.96, K.98, A.239, I.241, P.357, L.358, P.359 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.95, B:P.96, B:I.241, B:I.241 Hydrogen bonds: B:L.93, B:L.93, B:E.95 YL5.10: 8 residues within 4Å: Chain B: E.340, E.341, Y.344, M.348, L.364, R.368, Y.371, K.372 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.341, B:Y.344, B:R.368, B:Y.371 Hydrogen bonds: B:Y.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Pharmacophore Mapping of Thienopyrimidine-Based Monophosphonate (ThP-MP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase. J. Med. Chem. (2017)

Release Date

2017-03-15

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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