SMTL ID : 6gk0.1

HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH CLASS III HISTONE DEACETYLASE INHIBITOR

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.66, A.67, G.68, K.71, G.90, S.91, N.116, Y.118, N.152, N.183, K.226, T.254, N.255, T.256, S.276, G.277, L.280, V.304, G.305, G.306, L.326, Y.327, T.328 Ligands: DOR.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.116, A:Y.118, A:Y.327 Hydrogen bonds: A:A.67, A:K.71, A:S.91, A:S.91, A:N.152, A:K.226, A:K.226, A:K.226, A:N.255, A:G.277, A:G.306, A:Y.327, A:T.328 Water bridges: A:A.67, A:G.305, A:V.307, A:V.307, A:V.307

1 x DOR: (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Non-covalent)

DOR.2: 13 residues within 4Å: Chain A: K.71, N.116, R.117, Y.118, G.119, F.120, N.183, S.186, P.187, N.188, N.255, T.256 Ligands: FMN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.120 Hydrogen bonds: A:N.116, A:N.116, A:N.116, A:Y.118, A:G.119, A:F.120, A:N.183, A:N.188, A:N.255, A:N.255, A:T.256 Water bridges: A:S.186, A:S.186 Salt bridges: A:K.71

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 6 residues within 4Å: Chain A: Q.139, A.140, T.143, L.176, A.177, D.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.178 ACY.4: 4 residues within 4Å: Chain A: D.282, T.285, Q.286, R.289 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.282, A:Q.286 Hydrogen bonds: A:Q.286 Salt bridges: A:R.289 ACY.13: 4 residues within 4Å: Chain A: A.42, R.43, F.44, R.343 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.43, A:F.44 Water bridges: A:F.44, A:G.339, A:R.343 Salt bridges: A:R.343 ACY.14: 1 residues within 4Å: Chain A: R.131 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.131

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: P.94, K.95, L.125, E.168 No protein-ligand interaction detected (PLIP)

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

SO4.6: 3 residues within 4Å: Chain A: R.216, V.218, H.219 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.216, A:H.219 SO4.7: 2 residues within 4Å: Chain A: R.217, R.220 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.217, A:R.217 Salt bridges: A:R.220 SO4.8: 4 residues within 4Å: Chain A: T.232, Q.234, D.235 Ligands: SO4.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.232, A:T.232 Water bridges: A:S.233 SO4.10: 3 residues within 4Å: Chain A: T.232, S.233 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.233 Water bridges: A:Q.234 SO4.11: 3 residues within 4Å: Chain A: S.233, K.236, E.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.233 Water bridges: A:K.236, A:K.236, A:E.290 Salt bridges: A:K.236

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

CL.9: 2 residues within 4Å: Chain A: R.269, S.270 Ligand excluded by PLIP

1 x DDQ: DECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DDQ.12: 8 residues within 4Å: Chain A: E.24, R.28, H.72, P.96, Q.97, N.121, S.122, H.123 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.121 Hydrogen bonds: A:N.121

1 x F1W: 4-~{tert}-butyl-~{N}-[[4-[5-(dimethylamino)pentanoylamino]phenyl]carbamothioyl]benzamide(Non-covalent)

F1W.15: 15 residues within 4Å: Chain A: Y.9, L.13, M.14, L.17, Q.18, P.23, A.26, H.27, A.30, L.38, L.39, V.105, Y.327, T.331, P.335 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.23, A:H.27, A:L.39, A:P.335 Hydrogen bonds: A:Q.18, A:L.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ladds, M.J.G.W. et al., Exploitation of dihydroorotate dehydrogenase (DHODH) and p53 activation as therapeutic targets: A case study in polypharmacology. J.Biol.Chem. (2020)

Release Date

2019-11-27

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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