SMTL ID : 7x62.1

Crystal structure of AtHPPD-Y191051 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 9XI.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.3 CO.4: 4 residues within 4Å: Chain B: H.198, H.280, E.366 Ligands: 9XI.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.198, B:H.280, B:E.366, H2O.11

2 x 9XI: 1,5-dimethyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-phenyl-quinazoline-2,4-dione(Non-covalent)

9XI.2: 18 residues within 4Å: Chain A: H.198, V.200, L.237, S.239, P.252, N.254, Q.265, H.280, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.1, MPD.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.252, A:F.353, A:F.353, A:F.364, A:F.391, A:F.396, A:F.396 Water bridges: A:Q.279, A:Q.351 9XI.5: 18 residues within 4Å: Chain B: H.198, V.200, L.237, S.239, P.252, N.254, Q.265, H.280, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.4, MPD.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.252, B:F.353, B:F.353, B:F.364, B:F.391, B:F.396, B:F.396 Water bridges: B:Q.279, B:Q.351

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: Q.265, M.307, P.356, P.361, F.364 Ligands: 9XI.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.265 Hydrogen bonds: A:P.361 MPD.6: 6 residues within 4Å: Chain B: Q.265, M.307, P.356, P.361, F.364 Ligands: 9XI.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.265 Hydrogen bonds: B:P.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Discovery of Subnanomolar Inhibitors of 4-Hydroxyphenylpyruvate Dioxygenase via Structure-Based Rational Design. J.Agric.Food Chem. (2023)

Release Date

2022-06-01

Peptides

4-hydroxyphenylpyruvate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-hydroxyphenylpyruvate dioxygenase

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