SMTL ID : 6r06.1

T. CRUZI FPPS IN COMPLEX WITH (3S,4S)-4-(3,4-dimethylphenoxy)-1-(prop-2-yn-1-yl)piperidin-3-ol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

4 x JMN: (3~{S},4~{S})-4-(3,4-dimethylphenoxy)-1-prop-2-ynyl-piperidin-3-ol(Covalent)(Non-covalent)

JMN.1: 14 residues within 4Å: Chain A: Y.96, L.97, E.99, D.100, T.165, A.166, Q.169, K.209, T.210, Y.213, Q.249 Chain B: N.128, I.131 Ligands: SO4.6 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.96, A:Y.96, A:Y.96, A:E.99, A:D.100, A:T.165, A:A.166, A:Q.169, A:Q.169, A:T.210, B:I.131, B:I.131 pi-Stacking: A:Y.96 JMN.2: 6 residues within 4Å: Chain A: L.10, Y.13, D.14, Q.17, D.43, L.47 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.10, A:L.10, A:D.43, A:L.47, A:L.47 Hydrogen bonds: A:D.43 Water bridges: A:Q.17 Salt bridges: A:D.14 JMN.8: 14 residues within 4Å: Chain A: N.128, I.131 Chain B: Y.96, L.97, E.99, D.100, T.165, A.166, Q.169, K.209, T.210, Y.213, Q.249 Ligands: SO4.13 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.96, B:Y.96, B:Y.96, B:E.99, B:D.100, B:T.165, B:A.166, B:Q.169, B:Q.169, B:T.210, A:I.131, A:I.131 Hydrogen bonds: B:Y.213 pi-Stacking: B:Y.96 JMN.9: 6 residues within 4Å: Chain B: L.10, Y.13, D.14, Q.17, D.43, L.47 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.10, B:L.10, B:D.43, B:L.47, B:L.47 Hydrogen bonds: B:D.43 Water bridges: B:Q.17 Salt bridges: B:D.14

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: D.100, D.104, Q.169 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.100, A:D.104, H2O.1, H2O.1, H2O.2 ZN.4: 3 residues within 4Å: Chain A: D.252, D.256 Ligands: SO4.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.252, H2O.1, H2O.2 ZN.10: 3 residues within 4Å: Chain B: D.100, D.104, Q.169 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.10, H2O.10, H2O.12 ZN.11: 3 residues within 4Å: Chain B: D.252, D.256 Ligands: SO4.13 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.252, H2O.10, H2O.12

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

SO4.5: 6 residues within 4Å: Chain A: G.49, K.50, Y.51, F.52, R.53, Q.93 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.50, A:Y.51, A:F.52 Water bridges: A:R.53, A:R.53, A:R.53, A:E.90, A:Q.93, A:R.110 Salt bridges: A:R.53 SO4.6: 7 residues within 4Å: Chain A: D.172, K.209, Q.249, D.252, K.275 Ligands: JMN.1, ZN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.172, A:Q.249 Water bridges: A:K.275, A:K.275 Salt bridges: A:K.209, A:K.275 SO4.12: 6 residues within 4Å: Chain B: G.49, K.50, Y.51, F.52, R.53, Q.93 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.50, B:Y.51, B:F.52 Water bridges: B:R.53, B:R.53, B:R.53, B:E.90, B:Q.93, B:R.110 Salt bridges: B:R.53 SO4.13: 7 residues within 4Å: Chain B: D.172, K.209, Q.249, D.252, K.275 Ligands: JMN.8, ZN.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.172, B:Q.249 Water bridges: B:D.172, B:D.253, B:K.275, B:K.275 Salt bridges: B:K.209, B:K.275

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 2 residues within 4Å: Chain A: Q.23, H.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.23 Salt bridges: A:K.27, A:H.143 ACT.14: 2 residues within 4Å: Chain B: Q.23, H.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.23 Water bridges: B:H.143 Salt bridges: B:K.27, B:H.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrick, J.K. et al., Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery. Thesis (2019)

Release Date

2020-04-01

Peptides

Farnesyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl diphosphate synthase

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