SMTL ID : 6cjg.1

Human dihydroorotate dehydrogenase bound to napthyridine inhibitor 46

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 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 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:N.113, A:Y.115 Hydrogen bonds: A:A.64, A:K.68, A:S.88, A:S.88, A:N.149, A:K.223, A:K.223, A:N.252, A:G.274, A:G.303, A:Y.324, A:T.325, A:T.325 Water bridges: A:G.302, A:V.304, A:V.304 pi-Stacking: A:Y.324

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 12 residues within 4Å: Chain A: K.68, N.113, R.114, Y.115, G.116, F.117, N.180, S.183, P.184, 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 F51: 2-([1,1'-biphenyl]-4-yl)-3-methyl-1,7-naphthyridine-4-carboxylic acid(Non-covalent)

F51.3: 14 residues within 4Å: Chain A: Y.6, M.11, Q.15, P.20, A.23, H.24, A.27, F.30, L.35, L.36, R.104, Y.324, T.328, P.332 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.6, A:Q.15, A:A.23, A:A.27, A:F.30, A:L.36, A:T.328, A:P.332 Hydrogen bonds: A:Q.15, A:Y.324, A:T.328 Salt bridges: A:R.104

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: D.279, T.282, Q.283, R.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.286, A:E.312 Water bridges: A:R.286

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

SO4.5: 3 residues within 4Å: Chain A: R.213, V.215, H.216 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.215 Salt bridges: A:R.213, A:H.216

1 x ZWI: 3-[decyl(dimethyl)ammonio]propane-1-sulfonate(Non-covalent)

ZWI.6: 3 residues within 4Å: Chain A: D.2, Y.6, F.30 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Madak, J.T. et al., Design, Synthesis, and Biological Evaluation of 4-Quinoline Carboxylic Acids as Inhibitors of Dihydroorotate Dehydrogenase. J. Med. Chem. (2018)

Release Date

2018-05-23

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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