SMTL ID : 6vtn.1

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM557

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x RL7: N-cyclopropyl-4-{[2-fluoro-4-(trifluoromethyl)phenyl]methyl}-3-methyl-1H-pyrrole-2-carboxamide(Non-covalent)

RL7.1: 22 residues within 4Å: Chain A: Y.30, F.33, L.34, C.37, L.38, G.43, E.44, C.46, H.47, L.49, F.50, L.53, F.89, I.125, R.127, I.134, Y.360, L.363, V.364, G.367, M.368 Ligands: FMN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.34, A:L.38, A:F.50, A:F.50, A:I.125, A:R.127, A:I.134, A:V.364 Hydrogen bonds: A:H.47, A:H.47, A:R.127 Halogen bonds: A:C.37

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 29 residues within 4Å: Chain A: A.86, A.87, G.88, K.91, G.110, T.111, I.125, I.134, N.136, C.138, F.140, S.173, N.204, K.261, S.289, N.290, T.291, S.309, G.310, L.313, S.337, G.338, G.339, I.340, L.359, Y.360, S.361 Ligands: RL7.1, ORO.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.134, A:N.136, A:Y.360 Hydrogen bonds: A:K.91, A:T.111, A:T.111, A:S.173, A:N.204, A:K.261, A:N.290, A:S.309, A:G.310, A:G.339, A:I.340, A:Y.360, A:S.361, A:S.361 Water bridges: A:G.338, A:G.338, A:G.338, A:Q.358 pi-Stacking: A:Y.360

1 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 12 residues within 4Å: Chain A: K.91, N.136, C.138, G.139, F.140, N.204, S.207, P.208, N.209, N.290, T.291 Ligands: FMN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.140 Hydrogen bonds: A:N.136, A:N.136, A:N.136, A:C.138, A:G.139, A:F.140, A:N.204, A:N.209, A:N.290, A:N.290, A:T.291 Salt bridges: A:K.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kokkonda, S. et al., Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria. J.Med.Chem. (2020)

Release Date

2020-04-22

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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