SMTL ID : 6oah.1

Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02-78

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Y.162, R.163, K.166, Y.175 Chain B: E.180, L.183, Q.184 No protein-ligand interaction detected (PLIP) GOL.5: 7 residues within 4Å: Chain A: E.180, L.183, Q.184 Chain B: Y.162, R.163, K.166, Y.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.175

4 x M2V: [(1R)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-phenylethyl]phosphonic acid(Non-covalent)

M2V.2: 11 residues within 4Å: Chain A: N.81, R.82, T.85, S.227, F.228, F.261, Q.264, L.366, K.369, I.370, K.372 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.81, A:R.82, A:F.228, A:F.261, A:I.370, A:K.372 Hydrogen bonds: A:K.369, A:K.369 Water bridges: A:N.81, A:N.81 M2V.3: 7 residues within 4Å: Chain A: A.334, L.337, Q.338, E.340, E.341, Y.371, K.372 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.337, A:E.341, A:Y.371 M2V.6: 11 residues within 4Å: Chain B: N.81, R.82, T.85, S.227, F.228, F.261, Q.264, L.366, K.369, I.370, K.372 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:N.81, B:R.82, B:F.228, B:F.261, B:I.370, B:K.372 Hydrogen bonds: B:K.369, B:K.369 Water bridges: B:N.81, B:N.81 M2V.7: 7 residues within 4Å: Chain B: A.334, L.337, Q.338, E.340, E.341, Y.371, K.372 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.337, B:E.341, B:Y.371

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

PO4.4: 5 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.79, A:Q.118 Water bridges: A:Y.80, A:N.81, A:R.82, A:R.82, A:E.115 Salt bridges: A:R.82, A:R.135 PO4.8: 5 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.79, B:Q.118 Water bridges: B:Y.80, B:N.81, B:R.82, B:R.82, B:E.115 Salt bridges: B:R.82, B:R.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Y. et al., Chirality-Driven Mode of Binding of alpha-Aminophosphonic Acid-Based Allosteric Inhibitors of the Human Farnesyl Pyrophosphate Synthase (hFPPS). J.Med.Chem. (2019)

Release Date

2019-11-06

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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