SMTL ID : 6e0b.1

Plasmodium falciparum dihydroorotate dehydrogenase C276F mutant bound with triazolopyrimidine-based inhibitor DSM1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x JZ8: 5-methyl-7-(naphthalen-2-ylamino)-1H-[1,2,4]triazolo[1,5-a]pyrimidine-3,8-diium(Non-covalent)

JZ8.1: 20 residues within 4Å: Chain A: L.34, C.37, L.38, G.43, C.46, H.47, F.50, L.51, G.54, L.59, F.89, C.95, I.99, L.102, I.125, R.127, L.363, V.364, G.367, M.368 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.34, A:L.38, A:F.50, A:F.50, A:L.59, A:F.89, A:F.89, A:I.99 Hydrogen bonds: A:H.47, A:H.47, A:R.127

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 28 residues within 4Å: Chain A: A.86, A.87, G.88, K.91, G.110, T.111, I.125, I.134, N.136, F.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.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.125, A:N.136, A:F.138, 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:G.339, A:Y.360, A:S.361, A:S.361 Water bridges: A:E.108, A:G.338, A:G.338, A:G.338, A:I.340, 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, F.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:F.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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.179, T.180, V.181, N.182, D.185 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.181, A:N.182, A:N.182, A:D.185, A:D.185 GOL.5: 7 residues within 4Å: Chain A: K.55, G.93, V.94, N.151, L.154, F.155, R.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.151, A:F.155, A:R.158, A:R.158 GOL.6: 7 residues within 4Å: Chain A: N.24, E.26, F.27, P.60, Y.61, T.63 Ligands: LDA.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.24, A:E.26, A:Y.61, A:Y.61

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

LDA.7: 9 residues within 4Å: Chain A: E.26, L.29, Y.30, N.57, I.58, L.59, P.60, Y.61 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.30 Salt bridges: A:E.26 pi-Cation interactions: A:Y.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, J. et al., Identification and Mechanistic Understanding of Dihydroorotate Dehydrogenase Point Mutations in Plasmodium falciparum that Confer in Vitro Resistance to the Clinical Candidate DSM265. ACS Infect Dis (2019)

Release Date

2018-11-14

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial