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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? the chemical structure I want to create a PDB from 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). $\endgroup$
    – marcin
    Nov 2, 2022 at 19:58
  • $\begingroup$ 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 ? $\endgroup$
    – pippo1980
    Nov 27, 2022 at 15:09

2 Answers 2

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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 :

picture got with https://litemol.org/Viewer/

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 :

ligs

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 :

enter image description here

more about the compound at:

PDB Chemical Component 1YI

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

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