.SDF file to .PDB file

Use OpenBabel.

Something like babel -isdf file_in.sdf -opdb file_out.pdb.

Bizarrely, Obabel seems to have written a PDB that was incorrectly spaced for the OP as seen in Error pasing the following line in pdb

If you can use python, rdkit is a great package for cheminformatics —best installed via conda though.

It allows you do all sorts of things, such as match substructures, embed conformers, edit compounds, compute advanced parameters and many forms of shape & colour finger-/foot-printings.

Given a multi-compound sdf you can read each individual molecule and write them out as PDBs.

from rdkit import Chem
with i, mol in enumerate(Chem.SDMolSupplier('in.sdf')):
    Chem.MolToPDBFile(f'out_{i}.pdb')

We can be fancier with the output name

from rdkit import Chem
import re
with mol in Chem.SDMolSupplier('in.sdf'):
    # The headerline of a mol file is retrieved oddly.
    name = mol.GetProp('_Name')
    # make filename safe
    slugify = lambda name: re.sub(r'[\W_.-]+', '-', name)
    Chem.MolToPDBFile(f'{slugify(name)}.pdb')

To specify what name (e.g. CA) each atom gets and what is the residue name, chain and residue position —information absent in the sdf, it gets a bit odd.

  names = [' CA ', ' CB ', ' CG ', ' CD '] # say
  for i, atom in enumerate(mol.GetAtoms()):
        info = Chem.AtomPDBResidueInfo(names[i], # or whatever.
                                       residueName='LIG')

For more see this blog post.