SMTL ID : 5mvc.1

Crystal structure of potent human Dihydroorotate Dehydrogenase inhibitors based on hydroxylated azole scaffolds

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 24 residues within 4Å: Chain A: A.89, A.90, G.91, K.94, G.113, S.114, N.139, Y.141, N.175, N.206, K.249, T.277, N.278, T.279, S.299, G.300, L.303, V.327, G.328, G.329, L.349, Y.350, T.351 Ligands: ORO.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.139, A:Y.141, A:Y.350, A:Y.350 Hydrogen bonds: A:A.90, A:K.94, A:S.114, A:S.114, A:N.175, A:N.206, A:K.249, A:K.249, A:N.278, A:S.299, A:G.300, A:G.329, A:Y.350, A:T.351 Water bridges: A:A.90, A:G.328, A:G.328

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 12 residues within 4Å: Chain A: K.94, N.139, R.140, Y.141, G.142, F.143, N.206, S.209, P.210, N.278, T.279 Ligands: FMN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.139, A:Y.141, A:G.142, A:F.143, A:N.206, A:N.278, A:N.278, A:T.279 Salt bridges: A:K.94

1 x Y9B: 4-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]-1,2,5-thiadiazole-3-carboxamide(Non-covalent)

Y9B.3: 16 residues within 4Å: Chain A: Y.32, M.37, L.40, Q.41, P.46, A.49, H.50, A.53, F.56, T.57, L.61, L.62, R.130, L.353, T.354, P.358 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.53, A:F.56, A:L.62, A:P.358 Hydrogen bonds: A:Q.41, A:R.130, A:R.130, A:T.354 Water bridges: A:T.354

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

ACT.4: 4 residues within 4Å: Chain A: D.305, T.308, Q.309, R.312 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.309 Salt bridges: A:R.312 ACT.5: 6 residues within 4Å: Chain A: Q.162, A.163, T.166, L.199, A.200, D.201 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.162 Hydrogen bonds: A:D.201 Water bridges: A:A.163, A:E.167

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

CL.6: 2 residues within 4Å: Chain A: T.295, G.296 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: P.46, F.129, R.130, L.291 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: Q.159, P.198, H.242 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: Q.120, E.121, G.122 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: E.191, R.194 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sainas, S. et al., Design, synthesis, biological evaluation and X-ray structural studies of potent human dihydroorotate dehydrogenase inhibitors based on hydroxylated azole scaffolds. Eur J Med Chem (2017)

Release Date

2017-03-08

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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