SMTL ID : 4rxa.1

Crystal structure of human farnesyl diphosphate synthase in complex with BPH-1358

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 3F2: N,N'-bis[3-(4,5-dihydro-1H-imidazol-2-yl)phenyl]biphenyl-4,4'-dicarboxamide(Non-covalent)

3F2.1: 15 residues within 4Å: Chain A: K.9, K.52, N.54, R.55, L.57, T.58, V.61, E.65, F.234, D.238, V.335, G.338, L.339, K.342 Ligands: PO4.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.52, A:L.57, A:L.57, A:V.61, A:F.234, A:K.342, A:K.342 Hydrogen bonds: A:K.9, A:K.52, A:N.54 pi-Cation interactions: A:K.9 3F2.3: 15 residues within 4Å: Chain B: K.9, K.52, N.54, R.55, L.57, T.58, V.61, E.65, F.234, D.238, V.335, G.338, L.339, K.342 Ligands: PO4.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.52, B:L.57, B:L.57, B:V.61, B:F.234, B:K.342, B:K.342 Hydrogen bonds: B:K.9, B:K.52, B:N.54 pi-Cation interactions: B:K.9

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

PO4.2: 5 residues within 4Å: Chain A: G.51, K.52, Q.91, R.108 Ligands: 3F2.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.52, A:Q.91 Water bridges: A:Y.53, A:Y.53, A:R.55, A:Q.91 Salt bridges: A:R.108 PO4.4: 5 residues within 4Å: Chain B: G.51, K.52, Q.91, R.108 Ligands: 3F2.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.52, B:Q.91 Water bridges: B:Y.53, B:Y.53, B:R.55, B:Q.91 Salt bridges: B:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y.L. et al., Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries. ACS Med Chem Lett (2015)

Release Date

2015-04-15

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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