SMTL ID : 8vhl.1

Structure of DHODH in Complex with Ligand 17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 24 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 20 PLIP interactions: 20 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:N.185, 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:G.307

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 10 residues within 4Å: Chain A: K.73, N.118, R.119, Y.120, G.121, F.122, N.185, N.257, T.258 Ligands: FMN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.122 Hydrogen bonds: A:N.118, A:N.118, A:N.118, A:G.121, A:F.122, A:N.185, A:N.257, A:N.257 Salt bridges: A:K.73

1 x 01: N-(2-chloro-6-fluorophenyl)-4-[ethyl(2-hydroxyethyl)carbamamido]-5-fluoro-2-{[(2S)-1,1,1-trifluoropropan-2-yl]oxy}benzamide

01.3: 22 residues within 4Å: Chain A: Y.11, M.16, L.19, Q.20, L.23, P.25, A.28, H.29, L.31, A.32, F.35, T.36, L.40, L.41, F.71, V.107, R.109, V.116, Y.329, L.332, T.333, P.337 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.19, A:A.28, A:A.32, A:F.35, A:L.41, A:F.71, A:V.107, A:R.109, A:V.116, A:L.332, A:P.337 Hydrogen bonds: A:Q.20 Halogen bonds: A:A.32

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

ACT.4: 4 residues within 4Å: Chain A: D.284, T.287, Q.288, R.291 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.284, A:Q.288 Salt bridges: A:R.291 ACT.5: 1 residues within 4Å: Chain A: T.274 No protein-ligand interaction detected (PLIP) ACT.7: 6 residues within 4Å: Chain A: Q.141, A.142, T.145, L.178, A.179, D.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.145 Water bridges: A:A.142

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

SO4.6: 7 residues within 4Å: Chain A: E.26, H.29, R.30, K.73, H.74, Y.120, N.123 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.26, A:N.123 Water bridges: A:H.29, A:R.30, A:R.30, A:E.76 Salt bridges: A:H.29, A:R.30, A:H.74 SO4.10: 3 residues within 4Å: Chain A: R.218, V.220, H.221 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.218, A:H.221 SO4.11: 2 residues within 4Å: Chain A: K.200, R.204 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.204 Salt bridges: A:K.200, A:R.204

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: A.12, E.13, W.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.13 GOL.9: 4 residues within 4Å: Chain A: S.37, G.39, G.80, K.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.37 Water bridges: A:D.79, A:K.83 GOL.12: 6 residues within 4Å: Chain A: R.55, G.58, H.59, K.60, T.145, E.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.55, A:H.59, A:K.60, A:E.146 GOL.13: 3 residues within 4Å: Chain A: K.97, E.170, V.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.170, A:E.170 Water bridges: A:S.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeRatt, L.G. et al., Discovery of Alternative Binding Poses through Fragment-Based Identification of DHODH Inhibitors. Acs Med.Chem.Lett. (2024)

Release Date

2024-04-03

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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