SMTL ID : 8h6a.1

Crystal structure of AtHPPD complexed with YH21477

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 4 residues within 4Å: Chain A: H.198, H.280, E.366 Ligands: KWI.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.198, A:H.280, A:E.366, H2O.2 CO.3: 4 residues within 4Å: Chain B: H.198, H.280, E.366 Ligands: KWI.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.198, B:H.280, B:E.366, H2O.13

2 x KWI: 1-[(2-chlorophenyl)methyl]-3-methyl-N-(1-methyl-1,2,3,4-tetrazol-5-yl)-2-oxidanylidene-benzimidazole-4-carboxamide(Non-covalent)

KWI.2: 17 residues within 4Å: Chain A: H.198, V.200, S.239, P.252, N.254, H.280, L.340, Q.351, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.340, A:F.353, A:F.353, A:F.353, A:F.353, A:F.364, A:L.399 Hydrogen bonds: A:N.395 Water bridges: A:Q.351 pi-Stacking: A:F.396 KWI.4: 17 residues within 4Å: Chain B: H.198, V.200, S.239, P.252, N.254, H.280, L.340, Q.351, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.340, B:F.353, B:F.353, B:F.353, B:F.353, B:F.364, B:L.399 Hydrogen bonds: B:N.395 Water bridges: B:Q.351 pi-Stacking: B:F.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cai, Z.M. et al., Discovery of Tetrazolamide-benzimidazol-2-ones as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. J.Agric.Food Chem. (2024)

Release Date

2023-10-18

Peptides

4-hydroxyphenylpyruvate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-hydroxyphenylpyruvate dioxygenase

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