SMTL ID : 3zws.1

Structure of Human Dihydroorotate Dehydrogenase with a Bound Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: ORO.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:N.116, A:Y.118, A:Y.327, 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:S.276, A:G.277, A:G.306, A:Y.327, A:T.328, A:T.328 Water bridges: A:A.67, A:G.305, A:V.307, A:V.307, A:V.307

1 x ORO: OROTIC ACID(Non-covalent)

ORO.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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.120 Hydrogen bonds: 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 Water bridges: A:S.186, A:S.186 Salt bridges: A:K.71

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

SO4.3: 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 SO4.4: 5 residues within 4Å: Chain A: R.28, H.72, R.104, N.121, H.123 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.104, A:N.121, A:H.123 Water bridges: A:E.24, A:H.27, A:R.28, A:S.122 Salt bridges: A:R.28, A:H.72

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

CL.5: 3 residues within 4Å: Chain A: Q.136, P.175, H.219 Ligand excluded by PLIP

1 x AVQ: 2-[(2,5-DICHLOROBENZYL)SULFANYL]-5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-OL(Non-covalent)

AVQ.6: 13 residues within 4Å: Chain A: M.14, Q.18, P.23, A.26, H.27, A.30, F.69, V.105, R.107, Y.327, L.330, T.331, P.335 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.27, A:A.30, A:A.30, A:V.105 Hydrogen bonds: A:Q.18, A:R.107

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

ACT.7: 4 residues within 4Å: Chain A: D.282, T.285, Q.286, R.289 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.282, A:Q.286 Salt bridges: A:R.289 ACT.8: 6 residues within 4Å: Chain A: Q.139, A.140, T.143, L.176, A.177, D.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.143, A:D.178 Water bridges: A:E.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedingfield, P.T.P. et al., Factors Influencing the Specificity of Inhibitor Binding to the Human and Malaria Parasite Dihydroorotate Dehydrogenases. J.Med.Chem. (2012)

Release Date

2012-06-27

Peptides

DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL

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