SMTL ID : 9ccc.1

Crystal structure of human dihydroorotate dehydrogenase with new alkyne ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ORO: OROTIC ACID(Non-covalent)

ORO.1: 14 residues within 4Å: Chain A: K.72, N.117, R.118, Y.119, G.120, F.121, N.184, S.187, P.188, N.189, N.256, T.257, G.275 Ligands: FMN.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.121 Hydrogen bonds: A:N.117, A:N.117, A:Y.119, A:G.120, A:F.121, A:N.184, A:N.189, A:N.256, A:N.256, A:T.257 Salt bridges: A:K.72

1 x 01: N-{4-[(3-aminophenyl)ethynyl]phenyl}acetamide

01.2: 26 residues within 4Å: Chain A: Y.10, L.14, M.15, L.18, P.24, E.25, A.27, H.28, A.31, F.34, T.35, L.39, L.40, P.41, F.70, M.83, V.106, R.108, V.115, Y.119, Y.328, L.331, T.332, G.335, P.336 Ligands: FMN.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.10, A:A.27, A:A.31, A:L.40, A:F.70, A:L.331, A:T.332, A:P.336 Hydrogen bonds: A:T.35, A:Y.328 Water bridges: A:P.24

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

SO4.3: 2 residues within 4Å: Chain A: T.4, G.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.4 SO4.7: 1 residues within 4Å: Chain A: R.261 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.261, A:R.261, A:S.271

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.29, H.73, E.75, H.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.73, A:H.124 Water bridges: A:N.122 GOL.5: 4 residues within 4Å: Chain A: A.11, E.12, F.333, W.334 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.333 GOL.9: 9 residues within 4Å: Chain A: F.121, G.155, K.156, Y.167, N.184, V.185, S.186, S.187, T.190 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.167, A:V.185, A:T.190, A:T.190 Water bridges: A:K.156, A:K.156

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

CL.6: 2 residues within 4Å: Chain A: K.279, P.280 Ligand excluded by PLIP

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 31 residues within 4Å: Chain A: H.28, A.67, A.68, G.69, K.72, G.91, S.92, V.106, V.115, N.117, Y.119, F.121, N.153, N.184, K.227, T.255, N.256, T.257, S.277, G.278, L.281, V.305, G.306, G.307, V.308, L.327, Y.328, T.329, A.330 Ligands: ORO.1, 01.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.117, A:Y.119, A:Y.328, A:Y.328 Hydrogen bonds: A:K.72, A:S.92, A:S.92, A:N.153, A:K.227, A:T.255, A:N.256, A:G.278, A:G.307, A:Y.328, A:T.329, A:T.329 Water bridges: A:A.68, A:G.306, A:G.306, A:V.308, A:V.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purificacao, A.D. et al., Discovery of a novel alkyne-based scaffold inhibitor for human DHODH. To Be Published

Release Date

2025-06-25

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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