SMTL ID : 3n46.1

Human FPPS complex with NOV_980 and zoledronic acid/MG2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x 3N5: (2R)-1-[(benzyloxy)carbonyl]-2,3-dihydro-1H-indole-2-carboxylic acid(Non-covalent)

3N5.1: 12 residues within 4Å: Chain A: K.54, N.56, R.57, T.60, S.202, F.203, F.236, Q.239, L.341, K.344, I.345 Ligands: PO4.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.56, A:R.57, A:F.203, A:F.236, A:L.341, A:I.345 Hydrogen bonds: A:N.56 Water bridges: A:K.54 Salt bridges: A:K.54, A:R.57 pi-Cation interactions: A:K.54 3N5.7: 12 residues within 4Å: Chain B: K.54, N.56, R.57, T.60, S.202, F.203, F.236, Q.239, L.341, K.344, I.345 Ligands: PO4.12 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.56, B:R.57, B:F.203, B:F.236, B:L.341, B:I.345 Hydrogen bonds: B:N.56 Water bridges: B:K.54 Salt bridges: B:K.54, B:R.57 pi-Cation interactions: B:K.54

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.2: 13 residues within 4Å: Chain A: L.97, D.100, D.104, R.109, Q.168, K.197, T.198, Q.237, D.240, K.254 Ligands: MG.3, MG.4, MG.5 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.109, A:R.109, A:Q.237, A:D.240, A:K.254 Water bridges: A:S.106, A:S.106, A:S.106, A:S.106, A:Q.168, A:Q.168, A:K.197, A:K.197, A:K.254, A:K.254, A:K.254, A:K.254 pi-Cation interactions: A:K.197 ZOL.8: 13 residues within 4Å: Chain B: L.97, D.100, D.104, R.109, Q.168, K.197, T.198, Q.237, D.240, K.254 Ligands: MG.9, MG.10, MG.11 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:R.109, B:R.109, B:Q.237, B:D.240, B:K.254 Water bridges: B:D.104, B:D.104, B:S.106, B:S.106, B:Q.168, B:Q.168, B:K.197, B:K.197, B:T.198, B:D.244, B:D.244, B:K.254, B:K.254, B:K.254 pi-Cation interactions: B:K.197

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.100, D.104 Ligands: ZOL.2, MG.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, A:D.104, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: Q.237, D.240 Ligands: ZOL.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.240, H2O.1, H2O.2, H2O.3 MG.5: 5 residues within 4Å: Chain A: D.100, D.104, Q.168 Ligands: ZOL.2, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.100, A:D.104, H2O.1, H2O.2, H2O.3 MG.9: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: ZOL.8, MG.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.6, H2O.7 MG.10: 3 residues within 4Å: Chain B: Q.237, D.240 Ligands: ZOL.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.240, H2O.7, H2O.8, H2O.8 MG.11: 5 residues within 4Å: Chain B: D.100, D.104, Q.168 Ligands: ZOL.8, MG.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.6, H2O.7, H2O.8

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

PO4.6: 6 residues within 4Å: Chain A: G.53, K.54, R.57, Q.93, R.110 Ligands: 3N5.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.54, A:Y.55, A:Q.93, A:Q.93 Water bridges: A:R.57, A:R.57, A:R.57, A:R.57 Salt bridges: A:K.54, A:R.57, A:R.110 PO4.12: 6 residues within 4Å: Chain B: G.53, K.54, R.57, Q.93, R.110 Ligands: 3N5.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.54, B:Y.55, B:Q.93, B:Q.93 Water bridges: B:R.57, B:R.57, B:R.57, B:R.57 Salt bridges: B:K.54, B:R.57, B:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jahnke, W. et al., Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery. Nat.Chem.Biol. (2010)

Release Date

2010-08-18

Peptides

FARNESYL PYROPHOSPHATE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

FARNESYL PYROPHOSPHATE SYNTHASE

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