SMTL ID : 9eg9.1

Crystal structure of human dihydroorotate dehydrogenase in complex with lapachol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 25 residues within 4Å: Chain A: A.67, A.68, G.69, K.72, G.91, S.92, N.117, Y.119, N.153, N.184, K.227, T.255, N.256, T.257, S.277, G.278, L.281, V.305, G.306, G.307, L.327, Y.328, T.329 Ligands: ORO.2, 01.8 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:N.117, A:Y.119, A:Y.328 Hydrogen bonds: A:A.68, A:K.72, A:S.92, A:S.92, A:N.153, A:K.227, A:K.227, A:N.256, A:S.277, A:G.278, A:G.307, A:Y.328, A:T.329 Water bridges: A:A.68, A:G.306, A:V.308

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 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 Ligands: FMN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.117, 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

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

SO4.3: 2 residues within 4Å: Chain A: K.279, P.280 No protein-ligand interaction detected (PLIP) SO4.4: 3 residues within 4Å: Chain A: R.217, V.219, H.220 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.217, A:H.220 SO4.6: 2 residues within 4Å: Chain A: R.218, R.221 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.218, A:R.221 Salt bridges: A:R.221

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

ACT.5: 6 residues within 4Å: Chain A: Q.140, A.141, T.144, L.177, A.178, D.179 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.141

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: P.95, K.96, L.126, S.127, E.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.169 Water bridges: A:S.127, A:S.127, A:E.130 GOL.9: 1 residues within 4Å: Chain A: K.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.139 GOL.10: 3 residues within 4Å: Chain A: R.108, P.110, L.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.108 Water bridges: A:L.22, A:R.108

1 x 01: 2-hydroxy-3-(3-methylbut-2-en-1-yl)naphthalene-1,4-dione

01.8: 13 residues within 4Å: Chain A: M.15, L.18, Q.19, P.24, A.27, H.28, A.31, F.70, V.106, R.108, Y.328, T.332 Ligands: FMN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.18, A:Q.19, A:A.27, A:H.28, A:V.106, A:Y.328, A:T.332 Hydrogen bonds: A:Q.19, A:R.108 Water bridges: A:T.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purificacao, A.D. et al., Crystallographic Structure of Human Dihydroorotate Dehydrogenase in Complex with the Natural Product Inhibitor Lapachol. Acs Omega (2025)

Release Date

2025-08-06

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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