SMTL ID : 4ylw.1

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x 52Y: methyl (2Z)-cyano[3-(3-fluoro-4'-methoxybiphenyl-4-yl)-4-oxo-1,3-thiazolidin-2-ylidene]acetate(Non-covalent)

52Y.1: 16 residues within 4Å: Chain A: Y.32, L.36, L.40, L.52, A.53, F.56, T.57, L.61, L.62, P.63, I.88, F.92, M.105, Y.350, L.353, P.358 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.53, A:F.56, A:F.92, A:L.353, A:L.353, A:P.358 Hydrogen bonds: A:Y.32 Water bridges: A:A.53 Halogen bonds: A:L.61

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 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.3 23 PLIP interactions: 23 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:K.249, A:K.249, A:N.278, A:S.299, A:G.300, A:G.329, A:Y.350, A:T.351, A:T.351 Water bridges: A:A.90, A:G.328, A:V.330, A:V.330, A:V.330

1 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 12 residues within 4Å: Chain A: K.94, N.139, R.140, Y.141, G.142, F.143, N.206, S.209, N.211, N.278, T.279 Ligands: FMN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.139, A:N.139, A:Y.141, A:G.142, A:F.143, A:N.206, A:N.211, A:N.278, A:N.278 Water bridges: A:S.209, A:S.209 Salt bridges: A:K.94

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

SO4.4: 1 residues within 4Å: Chain A: R.154 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.154 Salt bridges: A:R.154 SO4.5: 3 residues within 4Å: Chain A: R.239, V.241, H.242 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.239 Salt bridges: A:R.239, A:H.242 SO4.6: 7 residues within 4Å: Chain A: Q.162, A.163, T.166, P.198, L.199, A.200, D.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.166 SO4.7: 1 residues within 4Å: Ligands: SO4.8 No protein-ligand interaction detected (PLIP) SO4.8: 2 residues within 4Å: Chain A: K.164 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.164 SO4.9: 4 residues within 4Å: Chain A: R.239, R.240, R.243 Ligands: SO4.13 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.240 Water bridges: A:R.239, A:R.239, A:V.241, A:R.243 Salt bridges: A:R.243 SO4.10: 3 residues within 4Å: Chain A: A.213, G.214, R.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.214, A:L.215 Water bridges: A:T.212, A:R.216 Salt bridges: A:R.216 SO4.11: 4 residues within 4Å: Chain A: A.65, R.66, F.67, G.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.65, A:R.66, A:F.67 Water bridges: A:G.362 SO4.12: 3 residues within 4Å: Chain A: K.301, P.302, R.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.301, A:R.304 Salt bridges: A:K.301 SO4.13: 3 residues within 4Å: Chain A: R.240, R.243 Ligands: SO4.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, D. et al., Crystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound. To Be Published

Release Date

2016-03-09

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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