SMTL ID : 7kzy.2 (1 other biounit)

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM778 (3-methyl-N-(1-(5-methyl-1H-pyrazol-3-yl)ethyl)-4-(1-(6-(trifluoromethyl)pyridin-3-yl)cyclopropyl)-1H-pyrrole-2-carboxamide)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x XCM: 3-methyl-N-[(1R)-1-(5-methyl-1H-pyrazol-3-yl)ethyl]-4-{1-[6-(trifluoromethyl)pyridin-3-yl]cyclopropyl}-1H-pyrrole-2-carboxamide(Non-covalent)

XCM.1: 25 residues within 4Å: Chain A: F.33, L.34, C.37, L.38, G.43, E.44, C.46, H.47, L.49, F.50, L.53, G.88, F.89, K.91, I.125, R.127, I.134, C.138, N.141, Y.360, L.363, V.364, G.367, M.368 Ligands: FMN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.50, A:I.125, A:I.125, A:V.364, A:V.364 Hydrogen bonds: A:H.47, A:H.47, A:R.127 pi-Stacking: A:H.47

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: XCM.1, ORO.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.125, A:I.134, A:N.136, A:Y.360 Hydrogen bonds: A:K.91, A:T.111, A:T.111, A:N.204, A:K.261, A:S.289, 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: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: 13 residues within 4Å: Chain A: K.91, N.136, S.137, C.138, G.139, F.140, N.204, S.207, P.208, N.209, N.290, T.291 Ligands: FMN.2 14 PLIP interactions: 14 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:N.209, A:N.290, A:N.290, A:T.291 Water bridges: A:S.207, A:S.207 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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