SMTL ID : 4oqv.1

High resolution crystal structure of human dihydroorotate dehydrogenase bound with DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 24 residues within 4Å: Chain A: A.63, A.64, G.65, K.68, G.87, S.88, N.113, Y.115, N.149, N.180, K.223, T.251, N.252, T.253, S.273, G.274, L.277, V.301, G.302, G.303, L.323, Y.324, T.325 Ligands: ORO.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:N.113, A:Y.115, A:Y.115, A:Y.324, A:Y.324 Hydrogen bonds: A:A.64, A:K.68, A:S.88, A:S.88, A:N.149, A:N.180, A:K.223, A:K.223, A:N.252, A:G.274, A:G.303, A:Y.324, A:T.325 Water bridges: A:A.64, A:G.302, A:V.304, A:V.304, A:V.304

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 10 residues within 4Å: Chain A: K.68, N.113, R.114, Y.115, G.116, F.117, N.180, N.252, T.253 Ligands: FMN.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.113, A:G.116, A:F.117, A:N.180, A:N.252, A:N.252, A:T.253 Salt bridges: A:K.68

1 x 2V6: N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine(Non-covalent)

2V6.3: 17 residues within 4Å: Chain A: Y.6, M.11, L.14, Q.15, P.20, E.21, A.23, H.24, A.27, L.36, V.102, R.104, V.111, Y.324, L.327, T.328, P.332 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.14, A:A.23 Hydrogen bonds: A:R.104 Water bridges: A:Y.324 Halogen bonds: A:Y.324

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 5 residues within 4Å: Chain A: A.137, T.140, L.173, A.174, D.175 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.140 ACY.5: 5 residues within 4Å: Chain A: D.279, T.282, Q.283, R.286, E.312 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.282 Water bridges: A:Q.283 Salt bridges: A:R.286

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: P.91, K.92, L.122, E.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.165

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain A: Q.133, Q.134, H.216 Ligands: NA.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.133, A:Q.134, A:Q.134 NA.9: 4 residues within 4Å: Chain A: Q.134, H.216 Ligands: NA.7, SO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.134

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain A: R.213, V.215, H.216 Ligands: NA.9 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.215 Salt bridges: A:R.213, A:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, X. et al., Fluorine Modulates Species Selectivity in the Triazolopyrimidine Class of Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors. J.Med.Chem. (2014)

Release Date

2014-06-04

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial