SMTL ID : 9cyz.1

Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL02134

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: E.180, L.183, Q.184, Y.187 Chain B: Y.162, R.163, K.166, Y.175 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:L.183, B:R.163 Hydrogen bonds: B:K.166, B:Y.175, B:Y.175 GOL.7: 8 residues within 4Å: Chain A: Y.162, R.163, K.166, Y.175 Chain B: E.180, L.183, Q.184, Y.187 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.166, A:Y.175 Water bridges: A:R.163, B:L.183

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

SO4.2: 4 residues within 4Å: Chain A: G.78, K.79, Q.118, R.135 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.79, A:Q.118 Water bridges: A:Y.80, A:R.82 Salt bridges: A:R.135 SO4.3: 6 residues within 4Å: Chain A: H.57, P.58, E.59, I.60 Chain B: S.217, Y.221 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.217, B:Y.221, A:H.57, A:E.59, A:E.59, A:I.60 Salt bridges: B:K.220 SO4.8: 4 residues within 4Å: Chain B: G.78, K.79, Q.118, R.135 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.79, B:Q.118 Water bridges: B:Y.80, B:R.82 Salt bridges: B:R.135 SO4.9: 6 residues within 4Å: Chain A: S.217, Y.221 Chain B: H.57, P.58, E.59, I.60 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.57, B:E.59, B:E.59, B:I.60, A:S.217 Salt bridges: A:K.220

6 x YL2: ({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)(Non-covalent)

YL2.4: 8 residues within 4Å: Chain A: F.260, L.337, E.340, E.341, Y.344, I.347, Y.371 Ligands: YL2.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.260, A:F.260, A:F.260, A:Y.344, A:I.347, A:I.347, A:Y.371 Hydrogen bonds: A:Y.371, A:Y.371 pi-Stacking: A:Y.344 YL2.5: 5 residues within 4Å: Chain A: Y.344, A.367, R.368, Y.371 Ligands: YL2.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.344, A:R.368, A:Y.371, A:Y.371 YL2.6: 18 residues within 4Å: Chain A: F.120, F.121, L.122, 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 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.120, A:F.121, A:F.121, A:F.121, A:A.124, A:D.125, A:T.189, A:E.190, A:Q.193, B:N.152, B:N.155 Hydrogen bonds: A:D.125, A:R.134, A:R.134, A:K.222, A:K.288, A:K.288 YL2.10: 8 residues within 4Å: Chain B: F.260, L.337, E.340, E.341, Y.344, I.347, Y.371 Ligands: YL2.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.260, B:F.260, B:F.260, B:Y.344, B:I.347, B:I.347, B:Y.371 Hydrogen bonds: B:Y.371 pi-Stacking: B:Y.344 YL2.11: 5 residues within 4Å: Chain B: Y.344, A.367, R.368, Y.371 Ligands: YL2.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.344, B:R.368, B:Y.371, B:Y.371 YL2.12: 18 residues within 4Å: Chain A: N.152, N.155 Chain B: F.120, F.121, L.122, 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 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.120, B:F.121, B:F.121, B:F.121, B:A.124, B:D.125, B:T.189, B:E.190, B:Q.193, A:N.152, A:N.155 Hydrogen bonds: B:D.125, B:D.125, B:D.129, B:R.134, B:R.134, B:K.222, B:Y.226, B:K.288, B:K.288

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, CL02134. 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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