SMTL ID : 7k2u.1

DHODH IN COMPLEX WITH LIGAND 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 25 residues within 4Å: Chain A: A.68, A.69, G.70, K.73, G.92, S.93, N.118, Y.120, N.154, N.185, K.228, T.256, N.257, T.258, S.278, G.279, L.282, V.306, G.307, G.308, L.328, Y.329, T.330 Ligands: ORO.2, VU7.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:N.118, A:Y.120, A:Y.329 Hydrogen bonds: A:A.69, A:K.73, A:S.93, A:S.93, A:N.154, A:K.228, A:K.228, A:N.257, A:G.279, A:G.308, A:Y.329, A:T.330, A:T.330 Water bridges: A:A.69, A:G.307, A:V.309

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 residues within 4Å: Chain A: K.73, N.118, R.119, Y.120, G.121, F.122, N.185, S.188, P.189, N.190, N.257, T.258 Ligands: FMN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.122 Hydrogen bonds: A:N.118, A:N.118, A:N.118, A:Y.120, A:G.121, A:F.122, A:N.185, A:N.190, A:N.257, A:N.257 Water bridges: A:S.188, A:S.188 Salt bridges: A:K.73

1 x VU7: 6-fluoro-2-(2'-fluoro[1,1'-biphenyl]-4-yl)-N-methoxy-3-methylquinoline-4-carboxamide(Non-covalent)

VU7.3: 21 residues within 4Å: Chain A: Y.11, L.15, M.16, L.19, Q.20, P.25, A.28, H.29, A.32, T.36, L.40, L.41, V.107, R.109, Y.329, L.332, T.333, F.334, P.337 Ligands: FMN.1, PGE.12 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.11, A:L.19, A:A.28, A:H.29, A:A.32, A:L.41, A:Y.329, A:T.333, A:T.333, A:P.337 Hydrogen bonds: A:R.109, A:T.333

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: K.280, P.281 No protein-ligand interaction detected (PLIP) ACT.5: 7 residues within 4Å: Chain A: Q.141, A.142, T.145, L.178, A.179, D.180 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.145 Water bridges: A:E.146 ACT.8: 1 residues within 4Å: Chain A: T.274 No protein-ligand interaction detected (PLIP) ACT.9: 2 residues within 4Å: Chain A: T.234, S.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.235 Water bridges: A:L.233, A:S.235, A:Q.236

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

SO4.6: 3 residues within 4Å: Chain A: R.218, V.220, H.221 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.218, A:V.220, A:V.220 Salt bridges: A:R.218, A:H.221 SO4.10: 1 residues within 4Å: Chain A: R.133 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.133 Salt bridges: A:R.133 SO4.11: 2 residues within 4Å: Chain A: R.30, H.125 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.74 Salt bridges: A:R.30, A:H.125 SO4.14: 3 residues within 4Å: Chain A: T.234, Q.236, D.237 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.234

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: E.26, H.29, R.30, K.73, H.74, Y.120, N.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.26, A:R.30, A:R.104, A:N.123 GOL.13: 7 residues within 4Å: Chain A: H.59, A.179, D.180, R.219, V.220, R.222 Ligands: ACT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.179, A:R.222

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 8 residues within 4Å: Chain A: Y.11, L.15, L.19, L.31, F.35, L.40, L.41 Ligands: VU7.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeRatt, L.G. et al., A carboxylic acid isostere screen of the DHODH inhibitor Brequinar. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-10-21

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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