SMTL ID : 5del.1

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM59

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 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: ORO.2, D59.3 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:S.173, A:N.204, A:K.261, A:N.290, A:S.309, A:G.310, A:S.337, A:G.338, A:G.339, A:Y.360, A:S.361, A:S.361 Water bridges: A:A.87, A:I.340, A:Q.358, A:Q.358, A:L.359 pi-Stacking: A:Y.360

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 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.290, T.291, G.307 Ligands: FMN.1 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

1 x D59: N-(3,5-dichlorophenyl)-2-methyl-3-nitrobenzamide(Non-covalent)

D59.3: 20 residues within 4Å: Chain A: L.34, L.38, G.43, E.44, C.46, H.47, F.50, L.51, L.59, F.89, I.99, L.102, I.125, R.127, Y.360, L.363, V.364, G.367, M.368 Ligands: FMN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.38, A:H.47, A:F.50, A:Y.360, A:V.364 Hydrogen bonds: A:H.47

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: K.55, G.93, V.94, I.96, N.151, L.154, F.155, R.158 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.55, A:F.155, A:R.158, A:R.158 Water bridges: A:G.93, A:D.97 GOL.6: 5 residues within 4Å: Chain A: D.179, T.180, V.181, N.182, D.185 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.179, A:V.181, A:N.182 Water bridges: A:T.180, A:N.182, A:N.182

1 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.5: 1 residues within 4Å: Chain A: E.26 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, X. et al., The X-ray structure of Plasmodium falciparum dihydroorotate dehydrogenase bound to a potent and selective N-phenylbenzamide inhibitor reveals novel binding-site interactions. Acta Crystallogr.,Sect.F (2015)

Release Date

2015-10-07

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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