SMTL ID : 9cz4.1

Crystal Structure (I) of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL03049

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.79, A:R.82, A:Q.118 Water bridges: A:Y.80, A:Y.80, A:Y.80, A:Y.80, A:Y.80, A:R.135 Salt bridges: A:R.135 SO4.5: 5 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.79, B:R.82, B:Q.118 Water bridges: B:Y.80, B:Y.80, B:Y.80, B:Y.80, B:Y.80, B:R.135 Salt bridges: B:R.135

4 x 01: {[(6-{4-[(1R)-2,2-difluorocyclopropyl]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)

01.2: 9 residues within 4Å: Chain A: F.260, F.261, L.337, E.340, Y.344, I.347, A.367, Y.371 Ligands: 01.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.260, A:F.260, A:E.340, A:Y.344, A:Y.344, A:I.347, A:Y.371, A:Y.371 Hydrogen bonds: A:Y.371, A:Y.371 pi-Stacking: A:Y.344 01.3: 6 residues within 4Å: Chain A: M.348, L.364, A.367, R.368, Y.371 Ligands: 01.2 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:Y.371 01.6: 9 residues within 4Å: Chain B: F.260, F.261, L.337, E.340, Y.344, I.347, A.367, Y.371 Ligands: 01.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.260, B:F.260, B:E.340, B:Y.344, B:Y.344, B:I.347, B:Y.371, B:Y.371 Hydrogen bonds: B:Y.371 pi-Stacking: B:Y.344 01.7: 6 residues within 4Å: Chain B: M.348, L.364, A.367, R.368, Y.371 Ligands: 01.6 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:Y.371

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: E.180, L.183, Q.184 Chain B: Y.162, R.163, K.166, Y.175 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:L.183 Hydrogen bonds: B:K.166 GOL.8: 7 residues within 4Å: Chain A: Y.162, R.163, K.166, Y.175 Chain B: E.180, L.183, Q.184 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.166, A:Y.175 Water bridges: B:L.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandya, V.R. et al., Crystal Structure (I) of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL03049. 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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