SMTL ID : 9cy2.1

Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.79, A:R.82, A:Q.118, A:Q.118 Water bridges: A:G.78, A:Y.80, A:Y.80, A:N.81, A:N.81, A:Q.118 Salt bridges: A:R.135 PO4.3: 5 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.79, B:R.82, B:Q.118, B:Q.118 Water bridges: B:Y.80, B:Y.80, B:N.81, B:N.81, B:Q.118, B:R.135 Salt bridges: B:R.135

2 x JD5: [({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)(Non-covalent)

JD5.2: 9 residues within 4Å: Chain A: M.257, F.260, F.261, L.337, E.340, Y.344, I.347, A.367, Y.371 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.260, A:F.261, A:E.340, A:Y.344, A:Y.344, A:I.347, A:I.347, A:A.367, A:Y.371, A:Y.371 Hydrogen bonds: A:E.340, A:E.340, A:Y.371, A:Y.371 JD5.4: 9 residues within 4Å: Chain B: M.257, F.260, F.261, L.337, E.340, Y.344, I.347, A.367, Y.371 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.260, B:F.261, B:E.340, B:Y.344, B:Y.344, B:I.347, B:I.347, B:A.367, B:Y.371, B:Y.371 Hydrogen bonds: B:E.340, B:Y.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandya, V.R. et al., Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120. To Be Published

Release Date

2025-10-29

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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