SMTL ID : 6vty.3 (3 other biounits)

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM483

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x RLA: ethyl 3,5-dimethyl-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxylate(Non-covalent)

RLA.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.390, L.393, V.394, G.397, M.398 Ligands: FMN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.38, A:F.50, A:F.50, A:F.50, A:F.89, A:I.125, A:I.134, A:V.394, A:V.394 Hydrogen bonds: A:H.47 Salt bridges: A:R.127

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.291, S.319, N.320, T.321, S.339, G.340, L.343, S.367, G.368, G.369, I.370, L.389, Y.390, S.391 Ligands: RLA.1, ORO.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.125, A:N.136, A:Y.390, A:Y.390 Hydrogen bonds: A:K.91, A:T.111, A:T.111, A:N.204, A:K.291, A:N.320, A:S.339, A:G.340, A:S.367, A:G.369, A:Y.390, A:S.391, A:S.391 Water bridges: A:A.87, A:E.108, A:G.368, A:G.368, A:G.368, A:I.370, A:Q.388, A:Q.388

1 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 13 residues within 4Å: Chain A: K.91, N.136, C.138, G.139, F.140, N.204, S.207, P.208, N.209, N.320, T.321, G.337 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:N.136, A:C.138, A:G.139, A:F.140, A:N.204, A:S.207, A:N.209, A:N.320, A:N.320, A:T.321 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
C

Dihydroorotate dehydrogenase (quinone), mitochondrial

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