SMTL ID : 4pvy.1

Crystal structure of human FPPS in complex with [({5-[4-(propan-2-yloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.125, D.129, Q.193, K.288 Ligands: MG.2, JD1.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.1, H2O.2 MG.2: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: MG.1, JD1.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.2 MG.3: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: JD1.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.2 MG.6: 6 residues within 4Å: Chain B: D.125, D.129, Q.193, K.288 Ligands: MG.7, JD1.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.10, H2O.10, H2O.11 MG.7: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: MG.6, JD1.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.10, H2O.11 MG.8: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: JD1.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.10, H2O.11, H2O.11

2 x JD1: [({5-[4-(propan-2-yloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)(Non-covalent)

JD1.4: 21 residues within 4Å: Chain A: F.120, F.121, A.124, D.125, M.128, D.129, R.134, T.189, E.190, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Chain B: N.152, N.155 Ligands: MG.1, MG.2, MG.3 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.120, A:F.121, A:F.121, A:A.124, A:T.189, A:E.190, A:Q.193, B:N.155 Hydrogen bonds: A:R.134, A:R.134, A:K.222, A:Y.226, A:Q.262 Water bridges: A:D.125, A:D.129, A:D.129, A:D.129, A:D.129, A:D.129, A:S.131, A:S.131, A:Q.193, A:K.222, A:D.269, A:D.269 JD1.9: 21 residues within 4Å: Chain A: N.152, N.155 Chain B: F.120, F.121, A.124, D.125, M.128, D.129, R.134, T.189, E.190, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.6, MG.7, MG.8 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.120, B:F.121, B:F.121, B:A.124, B:T.189, B:E.190, B:Q.193, A:N.155 Hydrogen bonds: B:R.134, B:R.134, B:K.222, B:Q.262 Water bridges: B:D.125, B:D.129, B:D.129, B:D.129, B:S.131, B:S.131, B:S.131, B:Q.193, B:K.222, B:K.279

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Y.162, R.163, K.166 Chain B: E.180, L.183, Q.184 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:R.163, A:K.166, B:L.183, B:Q.184 Hydrogen bonds: B:Q.184 GOL.10: 6 residues within 4Å: Chain A: E.180, L.183, Q.184 Chain B: Y.162, R.163, K.166 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:R.163, B:K.166, A:L.183, A:Q.184 Hydrogen bonds: A:Q.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase. PLoS ONE (2017)

Release Date

2015-04-15

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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