SMTL ID : 4n1z.1

Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with BPH-1222

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: R.55, Q.91, R.107, F.234, D.238, K.252 Ligands: PO4.5, N1Z.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.91, A:R.107 Salt bridges: A:K.52, A:R.55, A:K.252 PO4.5: 6 residues within 4Å: Chain A: G.51, K.52, R.55, Q.91, R.108 Ligands: PO4.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.52, A:Q.91 Water bridges: A:K.52, A:K.52, A:Y.53, A:R.55, A:R.55, A:R.55 Salt bridges: A:K.52, A:R.55, A:R.108 PO4.7: 8 residues within 4Å: Chain B: R.55, Q.91, R.107, F.234, D.238, K.252 Ligands: PO4.11, N1Z.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.91, B:R.107, B:D.238 Salt bridges: B:K.52, B:R.55, B:K.252 PO4.11: 6 residues within 4Å: Chain B: G.51, K.52, R.55, Q.91, R.108 Ligands: PO4.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.52, B:Q.91 Water bridges: B:K.52, B:K.52, B:Y.53, B:R.55, B:R.55, B:R.55 Salt bridges: B:K.52, B:R.55, B:R.108

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.238, D.256 Ligands: N1Z.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.238 MG.3: 5 residues within 4Å: Chain A: D.98, D.102, S.104 Ligands: MG.4, N1Z.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.98, A:D.102 MG.4: 6 residues within 4Å: Chain A: D.98, D.102, Q.166, D.169 Ligands: MG.3, N1Z.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.98, A:D.102 MG.8: 3 residues within 4Å: Chain B: D.238, D.256 Ligands: N1Z.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.238 MG.9: 5 residues within 4Å: Chain B: D.98, D.102, S.104 Ligands: MG.10, N1Z.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.98, B:D.102 MG.10: 6 residues within 4Å: Chain B: D.98, D.102, Q.166, D.169 Ligands: MG.9, N1Z.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.98, B:D.102

2 x N1Z: hydrogen [(1S)-1-hydroxy-2-(3-octyl-1H-imidazol-3-ium-1-yl)-1-phosphonoethyl]phosphonate(Non-covalent)

N1Z.6: 17 residues within 4Å: Chain A: F.93, F.94, D.98, D.102, R.107, E.163, Q.166, K.195, T.196, Q.235, D.238, K.252 Chain B: N.125 Ligands: PO4.1, MG.2, MG.3, MG.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.93, A:F.94, A:F.94, A:E.163, A:Q.166 Hydrogen bonds: A:R.107, A:R.107, A:Q.235, A:K.252 Water bridges: A:S.104 pi-Cation interactions: A:K.195 N1Z.12: 17 residues within 4Å: Chain A: N.125 Chain B: F.93, F.94, D.98, D.102, R.107, E.163, Q.166, K.195, T.196, Q.235, D.238, K.252 Ligands: PO4.7, MG.8, MG.9, MG.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.93, B:F.94, B:F.94, B:E.163, B:Q.166 Hydrogen bonds: B:R.107, B:R.107, B:Q.235, B:K.252 Water bridges: B:S.104 pi-Cation interactions: B:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, Y. et al., A combination therapy for KRAS-driven lung adenocarcinomas using lipophilic bisphosphonates and rapamycin. Sci Transl Med (2014)

Release Date

2014-12-10

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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