SMTL ID : 7kyv.1

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM634 (3-methyl-N-(1-(5-methylisoxazol-3-yl)ethyl)-4-(4-(trifluoromethyl)benzyl)-1H-pyrrole-2-carboxamide)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x XBY: 3-methyl-N-[(1R)-1-(5-methyl-1,2-oxazol-3-yl)ethyl]-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxamide(Non-covalent)

XBY.1: 25 residues within 4Å: Chain A: Y.11, F.14, L.15, C.18, L.19, G.24, E.25, C.27, H.28, L.30, F.31, L.34, G.69, F.70, K.72, I.106, R.108, I.115, C.119, Y.341, L.344, V.345, G.348, M.349 Ligands: FMN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.15, A:H.28, A:F.31, A:I.106, A:R.108 Hydrogen bonds: A:H.28, A:H.28, A:R.108

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 30 residues within 4Å: Chain A: A.67, A.68, G.69, K.72, G.91, T.92, I.106, I.115, N.117, C.119, F.121, S.154, N.185, K.242, S.270, N.271, T.272, S.290, G.291, L.294, S.318, G.319, G.320, I.321, L.340, Y.341, S.342, C.343 Ligands: XBY.1, ORO.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.106, A:N.117, A:Y.341 Hydrogen bonds: A:K.72, A:T.92, A:T.92, A:S.154, A:K.242, A:N.271, A:S.290, A:G.291, A:S.318, A:G.319, A:G.320, A:Y.341, A:S.342, A:S.342 Water bridges: A:I.321, A:I.321, A:I.321, A:Q.339 pi-Stacking: A:Y.341

1 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 13 residues within 4Å: Chain A: K.72, N.117, C.119, G.120, F.121, N.185, S.188, P.189, N.190, N.271, T.272, G.288 Ligands: FMN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.121 Hydrogen bonds: A:N.117, A:N.117, A:C.119, A:G.120, A:F.121, A:N.185, A:N.271, A:N.271, A:T.272 Water bridges: A:K.72, A:N.190 Salt bridges: A:K.72

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: N.101, A.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.101, A:A.102 GOL.5: 5 residues within 4Å: Chain A: E.7, F.8, P.41, Y.42, T.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.7, A:Y.42, A:Y.42 GOL.6: 7 residues within 4Å: Chain A: K.36, G.74, V.75, N.132, L.135, F.136, R.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.132, A:F.136, A:R.139, A:R.139 GOL.7: 8 residues within 4Å: Chain A: L.19, I.22, D.23, G.24, I.106, F.107, R.108, D.109 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.23, A:G.24, A:I.106, A:R.108, A:R.108, A:R.108 Water bridges: A:E.25

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
A

Dihydroorotate dehydrogenase (quinone), mitochondrial