SMTL ID : 6m6d.1

Structure of HPPD complexed with a synthesized inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: H.226, H.308, E.394 Ligands: NJX.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.226, A:H.308, A:E.394, H2O.2 CO.3: 4 residues within 4Å: Chain B: H.226, H.308, E.394 Ligands: NJX.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.226, B:H.308, B:E.394, H2O.11

2 x NJX: 1,5-dimethyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-(3-trimethylsilylprop-2-ynyl)quinazoline-2,4-dione(Non-covalent)

NJX.2: 18 residues within 4Å: Chain A: H.226, V.228, L.265, S.267, P.280, N.282, R.290, Q.293, H.308, F.381, F.392, E.394, F.419, G.420, N.423, F.424, L.427 Ligands: CO.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.265, A:P.280, A:F.381, A:F.392, A:F.419, A:F.424 Water bridges: A:Q.379 pi-Stacking: A:F.381, A:F.381 NJX.4: 18 residues within 4Å: Chain B: H.226, V.228, L.265, S.267, P.280, N.282, R.290, Q.293, H.308, F.381, F.392, E.394, F.419, G.420, N.423, F.424, L.427 Ligands: CO.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.265, B:P.280, B:F.381, B:F.392, B:F.419, B:F.424 Water bridges: B:Q.379 pi-Stacking: B:F.381, B:F.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qu, R.Y. et al., Structure-Guided Discovery of Silicon-Containing Subnanomolar Inhibitor of Hydroxyphenylpyruvate Dioxygenase as a Potential Herbicide. J.Agric.Food Chem. (2021)

Release Date

2021-03-10

Peptides

4-hydroxyphenylpyruvate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-hydroxyphenylpyruvate dioxygenase

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