SMTL ID : 7kyk.2 (3 other biounits)

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM589 (ethyl 3-methyl-4-((4-(trifluoromethyl)benzo[d]oxazol-7-yl)methyl)-1H-pyrrole-2-carboxylate)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x XAJ: ethyl 3-methyl-4-{[4-(trifluoromethyl)-1,3-benzoxazol-7-yl]methyl}-1H-pyrrole-2-carboxylate(Non-covalent)

XAJ.1: 22 residues within 4Å: Chain A: Y.30, D.31, F.33, L.34, C.37, L.38, G.43, 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.34, A:L.38, A:I.125, A:V.364 Hydrogen bonds: A:H.47 Water bridges: A:M.368 Salt bridges: A:H.47, A:R.127

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 30 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, C.362 Ligands: XAJ.1, ORO.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.125, A:N.136, A:Y.360 Hydrogen bonds: A:K.91, A:T.111, A:T.111, A:N.204, A:K.261, A:N.290, A:S.309, A:G.310, A:S.337, A:G.339, A:Y.360, A:S.361, A:S.361 Water bridges: A:A.87, A:E.108, A:G.338, A:G.338, A:I.340, A:Q.358, 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:C.138, A:G.139, A:F.140, A:N.204, A:S.207, 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

Palmer, M.J. et al., Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series. J.Med.Chem. (2021)

Release Date

2021-05-19

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dihydroorotate dehydrogenase (quinone), mitochondrial

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