SMTL ID : 6r05.1

T. CRUZI FPPS IN COMPLEX WITH N-BENZYL-6-METHYLPYRIDIN-2-AMINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 x JNE: 6-methyl-~{N}-(phenylmethyl)pyridin-2-amine(Non-covalent)

JNE.1: 6 residues within 4Å: Chain A: K.112, P.113, R.117, F.118, P.119 Chain B: E.185 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.112, A:P.113, A:F.118 pi-Stacking: A:F.118 Hydrogen bonds: B:E.185 JNE.8: 6 residues within 4Å: Chain A: E.185 Chain B: K.112, P.113, R.117, F.118, P.119 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.112, B:P.113, B:F.118 pi-Stacking: B:F.118 Hydrogen bonds: A:E.185 Water bridges: A:E.185

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

SO4.2: 8 residues within 4Å: Chain A: G.49, K.50, Y.51, F.52, R.53, Q.93, R.110 Ligands: ACT.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.50, A:Y.51, A:F.52, A:Q.93 Water bridges: A:R.53, A:R.53, A:R.53, A:E.90, A:Q.93, A:R.110, A:R.110 Salt bridges: A:R.53, A:R.110 SO4.9: 8 residues within 4Å: Chain B: G.49, K.50, Y.51, F.52, R.53, Q.93, R.110 Ligands: ACT.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.50, B:Y.51, B:F.52, B:Q.93 Water bridges: B:R.53, B:R.53, B:R.53, B:E.90, B:Q.93 Salt bridges: B:R.53, B:R.110

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: D.100, T.165, Q.169, K.209 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.100 DMS.10: 4 residues within 4Å: Chain B: D.100, T.165, Q.169, K.209 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.100

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

ACT.4: 4 residues within 4Å: Chain A: L.10, Y.13, D.14, L.47 No protein-ligand interaction detected (PLIP) ACT.5: 7 residues within 4Å: Chain A: K.50, F.52, Y.215, F.248, K.358, T.359 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.52 Hydrogen bonds: A:K.358 ACT.11: 4 residues within 4Å: Chain B: L.10, Y.13, D.14, L.47 No protein-ligand interaction detected (PLIP) ACT.12: 7 residues within 4Å: Chain B: K.50, F.52, Y.215, F.248, K.358, T.359 Ligands: SO4.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.52 Hydrogen bonds: B:Y.215, B:K.358

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 2 residues within 4Å: Chain A: D.100, D.104 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.7: 2 residues within 4Å: Chain A: D.252, D.256 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.252, H2O.1, H2O.1, H2O.2, H2O.7, H2O.7 ZN.13: 2 residues within 4Å: Chain B: D.100, D.104 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.11, H2O.11, H2O.12 ZN.14: 2 residues within 4Å: Chain B: D.252, D.256 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.252, H2O.11, H2O.12, H2O.12, H2O.17, H2O.17

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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