I want to create a PDB file of a drug that is given in a paper.
Can somebody share a tutorial or similar resources for a beginner-level user?
Thank you.
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1$\begingroup$ Could you add some context? What do you want the PDB file for? Do you have the structure of this molecule in another file format? (I didn't read the paper). $\endgroup$– marcinCommented Nov 2, 2022 at 19:58
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$\begingroup$ yep have same question. Wouldn' t a cif file better serve the use if needed for fitting a ligand into electron density ? Or you just nred to depict molecule in 3D ? $\endgroup$– pippo1980Commented Nov 27, 2022 at 15:09
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2 Answers
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You can use Image2Smiles tool. It produces smi format, then you can convert smi to pdb using openbabel.
If you just have a few figures, I suggest using PubChem Sketcher.
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or you could taket it from :
https://www.rcsb.org/structure/7WMV pdb file
HETATM 4865 C13 1YI A 701 106.585 114.218 112.698 1.00 74.13 C
HETATM 4866 C15 1YI A 701 106.050 112.633 114.547 1.00102.13 C
HETATM 4867 C17 1YI A 701 104.024 111.140 110.766 1.00 89.07 C
HETATM 4868 C20 1YI A 701 103.626 108.779 110.527 1.00 83.00 C
HETATM 4869 C21 1YI A 701 104.626 108.507 111.437 1.00 84.86 C
HETATM 4870 C22 1YI A 701 102.234 110.466 109.205 1.00 85.32 C
HETATM 4871 C24 1YI A 701 100.911 110.073 109.846 1.00 66.83 C
HETATM 4872 C26 1YI A 701 92.545 108.407 114.139 1.00 95.68 C
HETATM 4873 C28 1YI A 701 100.141 109.053 109.319 1.00 63.43 C
HETATM 4874 C11 1YI A 701 105.694 113.343 111.806 1.00 75.91 C
HETATM 4875 C12 1YI A 701 105.840 111.929 112.354 1.00 91.76 C
HETATM 4876 C14 1YI A 701 105.990 114.087 114.099 1.00 85.43 C
HETATM 4877 C16 1YI A 701 105.029 110.853 111.663 1.00 99.03 C
HETATM 4878 C18 1YI A 701 105.319 109.548 112.006 1.00100.47 C
HETATM 4879 C19 1YI A 701 103.333 110.096 110.188 1.00 81.96 C
HETATM 4880 C23 1YI A 701 104.801 110.649 116.200 1.00 88.38 C
HETATM 4881 C25 1YI A 701 102.892 107.590 109.921 1.00 99.79 C
HETATM 4882 C27 1YI A 701 100.517 110.745 110.979 1.00 88.80 C
HETATM 4883 C29 1YI A 701 98.556 109.383 111.080 1.00 77.66 C
HETATM 4884 C30 1YI A 701 97.245 109.006 111.756 1.00 83.68 C
HETATM 4885 C31 1YI A 701 97.108 107.503 111.935 1.00 85.27 C
HETATM 4886 C32 1YI A 701 99.328 110.410 111.602 1.00 90.75 C
HETATM 4887 C33 1YI A 701 98.954 108.713 109.937 1.00 76.18 C
HETATM 4888 C34 1YI A 701 96.107 107.127 113.039 1.00 98.03 C
HETATM 4889 C35 1YI A 701 94.780 107.913 113.042 1.00 92.89 C
HETATM 4890 C36 1YI A 701 91.696 107.883 115.298 1.00113.05 C
HETATM 4891 C37 1YI A 701 92.889 109.868 114.425 1.00 87.90 C
HETATM 4892 C38 1YI A 701 91.711 108.277 112.861 1.00 77.85 C
HETATM 4893 N8 1YI A 701 93.804 107.673 114.094 1.00 93.06 N
HETATM 4894 N9 1YI A 701 90.968 106.633 115.149 1.00106.00 N
HETATM 4895 O2 1YI A 701 105.306 111.885 113.648 1.00 99.43 O
HETATM 4896 O3 1YI A 701 106.050 113.444 110.457 1.00 80.66 O
HETATM 4897 O4 1YI A 701 106.560 115.552 112.284 1.00 86.11 O
HETATM 4898 O5 1YI A 701 106.634 114.878 115.050 1.00 99.48 O
HETATM 4899 O6 1YI A 701 94.512 108.703 112.208 1.00 84.41 O
HETATM 4900 O7 1YI A 701 91.625 108.487 116.316 1.00101.67 O
HETATM 4901 S1 1YI A 701 105.267 112.404 116.160 1.00121.62 S
picture :
obtained with : https://litemol.org/Viewer/
OOOPSSSSSSSSSS
realized that ligand in pdb its not the full ligand of your picture,
need to get it from Ligand page on RCSB_PDB : https://www.rcsb.org/ligand/1YI
download links highlighted in pics :
download /1YI_ideal.sdf convert via openbabel :
http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
result
WARNING: damped steplength 0.0184262 to 0.00725371
WARNING: damped steplength 0.00508674 to 0.00100138
COMPND 1YI
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 C LIG 1 3.537 -2.101 2.235 1.00 0.00 C
HETATM 2 C LIG 1 2.812 -4.346 1.266 1.00 0.00 C
HETATM 3 C LIG 1 2.262 -2.902 -2.712 1.00 0.00 C
HETATM 4 C LIG 1 0.447 -1.602 -3.663 1.00 0.00 C
HETATM 5 C LIG 1 0.405 -0.869 -2.474 1.00 0.00 C
HETATM 6 C LIG 1 1.522 -3.533 -5.065 1.00 0.00 C
HETATM 7 C LIG 1 0.305 -3.796 -5.950 1.00 0.00 C
HETATM 8 C LIG 1 -5.920 -1.833 -12.368 1.00 0.00 C
HETATM 9 C LIG 1 -0.581 -4.848 -5.684 1.00 0.00 C
HETATM 10 C LIG 1 2.908 -1.583 0.938 1.00 0.00 C
HETATM 11 C LIG 1 3.139 -2.484 -0.313 1.00 0.00 C
HETATM 12 C LIG 1 3.714 -3.615 2.273 1.00 0.00 C
HETATM 13 C LIG 1 2.202 -2.172 -1.496 1.00 0.00 C
HETATM 14 C LIG 1 1.247 -1.156 -1.414 1.00 0.00 C
HETATM 15 C LIG 1 1.366 -2.666 -3.802 1.00 0.00 C
HETATM 16 C LIG 1 1.091 -5.111 3.310 1.00 0.00 C
HETATM 17 C LIG 1 -0.531 -1.162 -4.707 1.00 0.00 C
HETATM 18 C LIG 1 -0.009 -2.939 -7.020 1.00 0.00 C
HETATM 19 C LIG 1 -2.131 -4.074 -7.418 1.00 0.00 C
HETATM 20 C LIG 1 -3.479 -4.118 -8.115 1.00 0.00 C
HETATM 21 C LIG 1 -3.492 -4.837 -9.473 1.00 0.00 C
HETATM 22 C LIG 1 -1.224 -3.051 -7.715 1.00 0.00 C
HETATM 23 C LIG 1 -1.778 -4.991 -6.415 1.00 0.00 C
HETATM 24 C LIG 1 -4.883 -4.859 -10.129 1.00 0.00 C
HETATM 25 C LIG 1 -5.503 -3.491 -10.484 1.00 0.00 C
HETATM 26 C LIG 1 -7.501 -1.753 -12.406 1.00 0.00 C
HETATM 27 C LIG 1 -5.427 -1.719 -13.834 1.00 0.00 C
HETATM 28 C LIG 1 -5.340 -0.600 -11.644 1.00 0.00 C
HETATM 29 N LIG 1 -5.408 -3.127 -11.821 1.00 0.00 N
HETATM 30 N LIG 1 -8.129 -2.821 -13.038 1.00 0.00 N
HETATM 31 O LIG 1 3.072 -3.897 -0.073 1.00 0.00 O
HETATM 32 O LIG 1 3.421 -0.244 0.755 1.00 0.00 O
HETATM 33 O LIG 1 2.698 -1.683 3.334 1.00 0.00 O
HETATM 34 O LIG 1 5.094 -3.922 1.972 1.00 0.00 O
HETATM 35 O LIG 1 -6.061 -2.821 -9.650 1.00 0.00 O
HETATM 36 O LIG 1 -8.120 -0.753 -12.076 1.00 0.00 O
HETATM 37 S LIG 1 1.026 -4.388 1.646 1.00 0.00 S
HETATM 38 C LIG 1 -9.774 -4.156 -16.922 1.00 0.00 C
HETATM 39 C LIG 1 -9.839 -1.879 -16.189 1.00 0.00 C
HETATM 40 N LIG 1 -9.383 -3.231 -15.850 1.00 0.00 N
HETATM 41 C LIG 1 -9.964 -3.665 -14.556 1.00 0.00 C
HETATM 42 C LIG 1 -9.568 -2.827 -13.310 1.00 0.00 C
CONECT 1 10 12 33
CONECT 2 31 12 37
CONECT 3 15 13
CONECT 4 17 15 5
CONECT 5 4 14
CONECT 6 7 15
CONECT 7 6 9 18
CONECT 8 28 29 27 26
CONECT 8
CONECT 9 7 23
CONECT 10 11 1 32
CONECT 11 13 10 31
CONECT 12 1 2 34
CONECT 13 3 14 11
CONECT 14 5 13
CONECT 15 6 4 3
CONECT 16 37
CONECT 17 4
CONECT 18 7 22
CONECT 19 23 22 20
CONECT 20 19 21
CONECT 21 20 24
CONECT 22 18 19
CONECT 23 9 19
CONECT 24 21 25
CONECT 25 35 24 29
CONECT 26 8 30 36
CONECT 27 8
CONECT 28 8
CONECT 29 25 8
CONECT 30 26 42
CONECT 31 11 2
CONECT 32 10
CONECT 33 1
CONECT 34 12
CONECT 35 25
CONECT 36 26
CONECT 37 2 16
CONECT 38 40
CONECT 39 40
CONECT 40 38 39 41
CONECT 41 40 42
CONECT 42 41 30
MASTER 0 0 0 0 0 0 0 0 42 0 42 0
END
picture here :
more about the compound at:
UPDATE
Last link doesnt work anymore :
Ligand Expo Ligand Expo is down from January 1-31, 2023. Requests to this service will return a 410 http error code (“Gone”). Please help us better understand which Ligand Expo features are utilized and should be integrated with RCSB.org by taking this survey.
Users can access CCD data in mmCIF format at https://files.wwpdb.org/pub/pdb/refdata/chem_comp/. For other data download during server downtime, please contact [email protected].
Can use : https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/1YI
