SMTL ID : 5mvd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 24 residues within 4Å: Chain A: A.62, A.63, G.64, K.67, G.86, S.87, N.112, Y.114, N.148, N.179, K.222, T.250, N.251, T.252, S.272, G.273, L.276, V.300, G.301, G.302, L.322, Y.323, T.324 Ligands: ORO.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.112, A:Y.114, A:Y.323, A:Y.323 Hydrogen bonds: A:A.63, A:K.67, A:S.87, A:S.87, A:N.148, A:K.222, A:K.222, A:N.251, A:S.272, A:G.273, A:G.302, A:Y.323, A:T.324, A:T.324 Water bridges: A:A.63, A:G.301, A:V.303

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 12 residues within 4Å: Chain A: K.67, N.112, R.113, Y.114, G.115, F.116, N.179, S.182, P.183, N.251, T.252 Ligands: FMN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.112, A:N.112, A:G.115, A:F.116, A:N.179, A:N.251, A:N.251 Water bridges: A:S.182, A:S.182 Salt bridges: A:K.67

1 x U91: 1,5-dimethyl-3-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]pyrazole-4-carboxamide(Non-covalent)

U91.3: 17 residues within 4Å: Chain A: Y.5, M.10, L.13, P.19, A.22, H.23, A.26, T.30, L.34, L.35, F.65, V.101, R.103, Y.323, L.326, T.327, P.331 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.5, A:H.23, A:A.26, A:L.35, A:Y.323, A:P.331 Hydrogen bonds: A:R.103, A:R.103

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

ACT.4: 6 residues within 4Å: Chain A: Q.135, A.136, T.139, L.172, A.173, D.174 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.135 Hydrogen bonds: A:T.139 ACT.5: 4 residues within 4Å: Chain A: D.278, T.281, Q.282, R.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.278 Water bridges: A:D.278, A:Q.282 Salt bridges: A:R.285

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

CL.6: 3 residues within 4Å: Chain A: Q.132, P.171, H.215 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: P.19, F.102, R.103, L.264 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: N.96 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