SMTL ID : 8vhm.1

Structure of DHODH in Complex with Fragment 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 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 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:N.118, A:Y.120, A:Y.329, 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:S.278, 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, A:A.331, A:A.331

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 01: N-{4-[(R)-cyclohexyl(hydroxy)methyl]phenyl}acetamide

01.3: 12 residues within 4Å: Chain A: Y.11, M.16, L.19, P.25, H.29, A.32, F.71, Y.329, L.332, T.333, G.336, P.337 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.11, A:L.19, A:H.29, A:A.32, A:F.71 Hydrogen bonds: A:P.25, A:L.332

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

SO4.4: 5 residues within 4Å: Chain A: A.44, R.45, F.46, G.341, R.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.45, A:F.46 Water bridges: A:G.341, A:G.341 Salt bridges: A:R.345 SO4.5: 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

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

ACT.6: 2 residues within 4Å: Chain A: T.234, Q.236 No protein-ligand interaction detected (PLIP) ACT.8: 3 residues within 4Å: Chain A: R.218, R.219, R.222 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.218 Hydrogen bonds: A:R.219, A:R.222 Salt bridges: A:R.219 ACT.9: 4 residues within 4Å: Chain A: D.284, T.287, Q.288, R.291 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.284, A:Q.288 Water bridges: A:Q.288 Salt bridges: A:R.291 ACT.11: 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:Q.138, A:T.145

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: T.234, S.235 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: G.193, R.195 Ligand excluded by PLIP

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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