SMTL ID : 9cze.1

High-Resolution Structure of Human DHODH for Molecular Replacement in Fragment Screening Campaign

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.217, V.219, H.220 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.219 Salt bridges: A:R.217, A:H.220

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 3 residues within 4Å: Chain A: T.233, Q.235, D.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.233 Water bridges: A:Q.235 DMS.3: 5 residues within 4Å: Chain A: D.283, T.286, Q.287, R.290, E.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.290 Salt bridges: A:D.283, A:E.316

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

ACY.4: 6 residues within 4Å: Chain A: Q.140, A.141, T.144, L.177, A.178, D.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.179 Water bridges: A:E.145, A:D.179 ACY.5: 4 residues within 4Å: Chain A: Q.137, Q.138, A.141, H.220 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.141 Hydrogen bonds: A:Q.137, A:Q.138 Salt bridges: A:H.220 ACY.6: 4 residues within 4Å: Chain A: A.43, R.44, F.45, G.340 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.44 Hydrogen bonds: A:R.44, A:F.45 Water bridges: A:G.340, A:G.340, A:G.340 ACY.7: 2 residues within 4Å: Chain A: T.233, S.234 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.233 Hydrogen bonds: A:S.234 Water bridges: A:L.232, A:S.234, A:Q.235 ACY.8: 2 residues within 4Å: Chain A: R.221 Ligands: ACY.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.221 ACY.9: 4 residues within 4Å: Chain A: R.217, R.218, R.221 Ligands: ACY.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.218 Water bridges: A:V.219 Salt bridges: A:R.221

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

CL.10: 3 residues within 4Å: Chain A: Q.137, P.176, H.220 Ligand excluded by PLIP

1 x ORO: OROTIC ACID(Non-covalent)

ORO.11: 12 residues within 4Å: Chain A: K.72, N.117, R.118, Y.119, G.120, F.121, N.184, S.187, N.189, N.256, T.257 Ligands: FMN.12 13 PLIP interactions: 13 interactions with chain A 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 Water bridges: A:S.187, A:S.187 Salt bridges: A:K.72

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.12: 24 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.11 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:N.117, A:Y.119, A:Y.328, 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: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, A:V.308, A:V.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purificacao, A.D. et al., Unexplored binding-sites on human DHODH identified by crystallographic fragment screening. To Be Published

Release Date

2025-10-29

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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