SMTL ID : 5zf9.1

Structure of human dihydroorotate dehydrogenase in complex with 280-12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 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 20 PLIP interactions: 20 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 Water bridges: A:A.90, A:G.328, A:V.330

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 residues within 4Å: Chain A: K.94, N.139, R.140, Y.141, G.142, F.143, N.206, S.209, P.210, N.211, N.278, T.279 Ligands: FMN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.143 Hydrogen bonds: A:N.139, A:N.139, A:G.142, A:F.143, A:N.206, A:N.211, A:N.278, A:N.278, A:T.279 Water bridges: A:S.209, A:S.209 Salt bridges: A:K.94

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

ACT.3: 4 residues within 4Å: Chain A: D.305, T.308, Q.309, R.312 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.305, A:Q.309 Salt bridges: A:R.312 ACT.4: 7 residues within 4Å: Chain A: E.47, H.50, R.51, K.94, H.95, Y.141, N.144 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.51, A:Y.141 Hydrogen bonds: A:N.144 Salt bridges: A:H.50, A:R.51, A:H.95 ACT.5: 6 residues within 4Å: Chain A: Q.162, A.163, T.166, L.199, A.200, D.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.201 ACT.6: 3 residues within 4Å: Chain A: T.255, Q.257, D.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.255, A:D.258

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

SO4.7: 2 residues within 4Å: Chain A: R.239, H.242 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.239, A:H.242 SO4.8: 2 residues within 4Å: Chain A: R.240, R.243 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.240, A:R.243 Salt bridges: A:R.243

1 x 9BR: 3-chloro-4,6-dihydroxy-2-methyl-5-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]benzaldehyde(Non-covalent)

9BR.9: 17 residues within 4Å: Chain A: M.37, L.40, Q.41, P.46, A.49, H.50, A.53, F.56, T.57, F.92, M.105, V.128, R.130, Y.350, L.353, T.354, P.358 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.40, A:L.40, A:Q.41, A:A.49, A:A.53, A:F.56, A:V.128, A:L.353, A:T.354 Hydrogen bonds: A:Q.41, A:R.130, A:Y.350, A:T.354 Water bridges: A:T.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazaki, Y. et al., Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol (2018)

Release Date

2018-09-26

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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