SMTL ID : 9cz5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

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

01.1: 9 residues within 4Å: Chain A: F.260, L.337, E.340, E.341, Y.344, I.347, A.367, Y.371 Ligands: 01.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.260, A:F.260, A:F.260, A:Y.344, A:Y.371, A:Y.371 Hydrogen bonds: A:Y.371, A:Y.371, A:Y.371 pi-Stacking: A:Y.344 01.2: 17 residues within 4Å: Chain A: F.120, F.121, A.124, D.125, M.128, D.129, R.134, T.189, E.190, Q.193, D.196, K.222, T.223, Y.226, K.288 Chain B: N.152, N.155 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:N.152, A:F.121, A:F.121, A:D.125, A:T.189, A:E.190, A:Q.193, A:Q.193 Halogen bonds: B:N.155 Hydrogen bonds: A:D.125, A:D.129, A:R.134, A:R.134, A:D.196, A:K.222 01.3: 3 residues within 4Å: Chain A: Y.344, R.368 Ligands: 01.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.344 pi-Stacking: A:Y.371 01.6: 9 residues within 4Å: Chain B: F.260, L.337, E.340, E.341, Y.344, I.347, A.367, Y.371 Ligands: 01.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.260, B:F.260, B:F.260, B:Y.344, B:Y.371, B:Y.371 Hydrogen bonds: B:Y.371, B:Y.371, B:Y.371 pi-Stacking: B:Y.344 01.7: 17 residues within 4Å: Chain A: N.152, N.155 Chain B: F.120, F.121, A.124, D.125, M.128, D.129, R.134, T.189, E.190, Q.193, D.196, K.222, T.223, Y.226, K.288 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.121, B:F.121, B:D.125, B:T.189, B:E.190, B:Q.193, B:Q.193, A:N.152 Hydrogen bonds: B:D.125, B:D.129, B:R.134, B:R.134, B:D.196, B:K.222, B:Y.226 Water bridges: B:D.196 Halogen bonds: A:N.155 01.8: 3 residues within 4Å: Chain B: Y.344, R.368 Ligands: 01.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.344 pi-Stacking: B:Y.371

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: E.180, L.183, Q.184 Chain B: Y.162, R.163, K.166 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:A.159, B:Y.162, A:L.183 GOL.9: 6 residues within 4Å: Chain A: Y.162, R.163, K.166 Chain B: E.180, L.183, Q.184 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:A.159, A:Y.162, B:L.183

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

SO4.5: 6 residues within 4Å: Chain A: G.78, K.79, Y.80, N.81, R.82, Q.118 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.79, A:Y.80, A:N.81, A:N.81 Water bridges: A:R.82, A:R.82, A:R.82, A:R.82 Salt bridges: A:R.82 SO4.10: 6 residues within 4Å: Chain B: G.78, K.79, Y.80, N.81, R.82, Q.118 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.79, B:Y.80, B:N.81, B:N.81 Water bridges: B:R.82, B:R.82, B:R.82, B:R.82 Salt bridges: B:R.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandya, V.R. et al., Crystal structure (II) 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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