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Converting Sdf Format To Pdb Format

How to I convert a 2D sdf format file into a correct 3D pdb format structure (to be used in docking with a protein). The compound is Ruthenium Red and the wikipedia and Pubchem link is given below. Please take the complex structure of RR into account while giving suggestions, I mean how to handle the Cl- ions, etc. What should be correct structure to be used in docking?

http://en.wikipedia.org/wiki/Ruthenium_red

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9548875&loc=ec_rcs

format conversion structure
• 33,822 views • link
updated by Southwan • Southwan • written by Tofayel Ahmed • Tofayel Ahmed

PDB format is no more "3D" than SDF is "2D". They are both file formats. Edited your title to reflect this.

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written by Neilfws Neilfws

3 answers

You can use Open Babel to convert between structure formats. It's available on most UNIX-like systems. For example using Ubuntu Linux:

sudo apt-get install openbabel
babel infile.mol outfile.pdb

I just ran it on a molfile obtained from this page and it worked fine.

The "correct" structure for docking is a more complicated question and one that you will have to investigate for yourself as part of your docking procedure (e.g. generating conformers).

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written by Neilfws Neilfws

If you use an unchecked (and probably only marginally optimized) OpenBabel or ChemExper structure of a multi-core ruthenium complex for a docking (or any other) study, you do not know what you are doing. Sorry to sound harsh, but this approach is incredibly naive. Most docking and coordinate generation/optimization algorithms are simply not parameterized for this kind of compound.

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written by Wolf Ihlenfeldt • Wolf Ihlenfeldt

Addinf to Wolf's comment, you not only need a structure but most likely a topology. And starting with the ions in the center of the complex, it will be tough. Most automatic topology builders will allow only 4 bonds per atoms for example.. It's possible, but very tough. I would consider changing these ions for something "similar" and parametrized and see if you get any decent results this way first..

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written by João Rodrigues João Rodrigues

Agree with the above. I addressed only the format conversion issue, but there's a lot more to docking.

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written by Neilfws Neilfws

I thank Wolf Ihlenfeldt, João Rodrigues, neilfws for their insightful replies. All the comments had addressed different practical issues and limitations in this case.

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written by Tofayel Ahmed • Tofayel Ahmed

dimkal has provided me with a 3D strc of the compound. He has used Maestro to generate 3D from 2D file obtained in the above link given by neilfws. The structure looks fine (as we don't have maestro in our dept. I can't use that strc) but 1 of my friend in my institute suggested me to run optimization in 'gaussview' to get optimized structure with proper charge. Would you guys like to comment on this?

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written by Tofayel Ahmed • Tofayel Ahmed

I'd suggest you first carefully check the documentation of your docking software to see whether it has a remote chance of getting reasonable scores when just one bond behind the outer shell of the docked complex heavy metal atoms are lurking, mixing in d-orbital contributions and other goodies... this is definitely not a standard system for routine docking studies.

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written by Wolf Ihlenfeldt • Wolf Ihlenfeldt

I had to dock a protein to a Vanadium compound. Since there was no topology whatsoever, I started by creating the parameters for the organic part of the compound with PRODRG. I then Pymol-built the rest of the ligand (Vanadium and a few coordinating waters) and restrained the bonds between the several "pieces" in the docking software itself. The Vanadium I was able to model because I had access to the source of the docking program (HADDOCK). After the topology for the ion was there, I ran the docking with the compound and it was pretty stable. However, the electrostatics were horrible!

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written by João Rodrigues João Rodrigues

This was likely due to bad parameterization and a very very rough strategy. Still, it corroborated the experimental results, so I was happy with the result, although I wouldn't trust the structure at all. Pulling such a "Macgyver" might not be the best thing but it might give you some hints. I'd say, first minimize the compound with Gaussian to get at least a stable conformation. Then if you can, either use a program that supports your ion, or try to substitute it for another. In this project I was involved, a colleague ran AutoDock using Phosphorous instead of Vanadium. I can't help further !

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written by João Rodrigues João Rodrigues

here's the 3d pdb coordinates (converted with Maestro) for the mol file found in neilfws' link.

TITLE     ruthred
MODEL        1
HETATM    1 RU1  UNK   900       0.040  -1.481  -0.071  1.00  0.00          Ru
HETATM    2 RU2  UNK   900      -3.058   0.541  -0.040  1.00  0.00          Ru
HETATM    3 RU3  UNK   900       2.783   0.897  -0.259  1.00  0.00          Ru
HETATM    4  O1  UNK   900      -1.803  -0.923   0.307  1.00  0.00           O
HETATM    5  O2  UNK   900       0.989   0.164  -0.565  1.00  0.00           O
HETATM    6  N1  UNK   900      -0.045  -2.031  -2.022  1.00  0.00           N1+
HETATM    7  N2  UNK   900      -1.189  -3.100  -0.177  1.00  0.00           N1+
HETATM    8  N3  UNK   900       0.392  -1.789   1.899  1.00  0.00           N1+
HETATM    9  N4  UNK   900       1.351  -3.032   0.081  1.00  0.00           N1+
HETATM   10  N5  UNK   900       2.706   2.913  -0.119  1.00  0.00           N1+
HETATM   11  N6  UNK   900       3.462   1.666  -2.003  1.00  0.00           N1+
HETATM   12  N7  UNK   900      -3.950  -0.258  -1.662  1.00  0.00           N1+
HETATM   13  N8  UNK   900      -4.873   1.441  -0.238  1.00  0.00           N1+
HETATM   14  N9  UNK   900      -4.352  -0.278   1.283  1.00  0.00           N1+
HETATM   15  N10 UNK   900      -2.750   1.824   1.485  1.00  0.00           N1+
HETATM   16  N11 UNK   900      -2.383   2.100  -1.111  1.00  0.00           N1+
HETATM   17  N12 UNK   900       3.789  -0.727  -0.903  1.00  0.00           N1+
HETATM   18  N13 UNK   900       2.540   0.959   1.744  1.00  0.00           N1+
HETATM   19  N14 UNK   900       4.619   0.887   0.610  1.00  0.00           N1+
HETATM   20  H1  UNK   900       3.702   0.872  -2.676  1.00  0.00           H
HETATM   21  H2  UNK   900       4.343   2.250  -1.842  1.00  0.00           H
HETATM   22  H3  UNK   900       2.710   2.262  -2.474  1.00  0.00           H
HETATM   23  H4  UNK   900       2.280   3.191   0.821  1.00  0.00           H
HETATM   24  H5  UNK   900       3.686   3.335  -0.183  1.00  0.00           H
HETATM   25  H6  UNK   900       2.082   3.324  -0.883  1.00  0.00           H
HETATM   26  H7  UNK   900       3.191  -1.237  -1.626  1.00  0.00           H
HETATM   27  H8  UNK   900       3.924  -1.366  -0.061  1.00  0.00           H
HETATM   28  H9  UNK   900       4.730  -0.490  -1.351  1.00  0.00           H
HETATM   29  H10 UNK   900       0.027  -3.086  -2.165  1.00  0.00           H
HETATM   30  H11 UNK   900       0.761  -1.563  -2.545  1.00  0.00           H
HETATM   31  H12 UNK   900      -0.965  -1.686  -2.442  1.00  0.00           H
HETATM   32  H13 UNK   900       0.034  -0.924   2.414  1.00  0.00           H
HETATM   33  H14 UNK   900       1.442  -1.873   2.102  1.00  0.00           H
HETATM   34  H15 UNK   900      -0.123  -2.657   2.252  1.00  0.00           H
HETATM   35  H16 UNK   900      -3.794  -0.874   1.973  1.00  0.00           H
HETATM   36  H17 UNK   900      -5.043  -0.919   0.779  1.00  0.00           H
HETATM   37  H18 UNK   900      -4.887   0.458   1.842  1.00  0.00           H
HETATM   38  H19 UNK   900      -2.548   1.923  -2.151  1.00  0.00           H
HETATM   39  H20 UNK   900      -2.885   2.998  -0.822  1.00  0.00           H
HETATM   40  H21 UNK   900      -1.335   2.216  -0.940  1.00  0.00           H
HETATM   41  H22 UNK   900      -1.989  -2.913  -0.861  1.00  0.00           H
HETATM   42  H23 UNK   900      -1.609  -3.289   0.787  1.00  0.00           H
HETATM   43  H24 UNK   900      -0.677  -3.982  -0.494  1.00  0.00           H
HETATM   44  H25 UNK   900       2.266  -2.690   0.516  1.00  0.00           H
HETATM   45  H26 UNK   900       0.963  -3.807   0.706  1.00  0.00           H
HETATM   46  H27 UNK   900       1.575  -3.439  -0.881  1.00  0.00           H
HETATM   47  H28 UNK   900      -3.295   2.731   1.342  1.00  0.00           H
HETATM   48  H29 UNK   900      -1.708   2.056   1.530  1.00  0.00           H
HETATM   49  H30 UNK   900      -3.035   1.379   2.413  1.00  0.00           H
HETATM   50  H31 UNK   900      -3.240  -0.874  -2.170  1.00  0.00           H
HETATM   51  H32 UNK   900      -4.779  -0.867  -1.375  1.00  0.00           H
HETATM   52  H33 UNK   900      -4.277   0.502  -2.339  1.00  0.00           H
HETATM   53  H34 UNK   900      -4.868   2.077  -1.097  1.00  0.00           H
HETATM   54  H35 UNK   900      -5.664   0.733  -0.353  1.00  0.00           H
HETATM   55  H36 UNK   900      -5.091   2.057   0.607  1.00  0.00           H
HETATM   56  H37 UNK   900       5.400   0.891  -0.119  1.00  0.00           H
HETATM   57  H38 UNK   900       4.765   1.747   1.226  1.00  0.00           H
HETATM   58  H39 UNK   900       4.669  -0.005   1.203  1.00  0.00           H
HETATM   59  H40 UNK   900       3.052   1.775   2.206  1.00  0.00           H
HETATM   60  H41 UNK   900       2.893   0.030   2.131  1.00  0.00           H
HETATM   61  H42 UNK   900       1.498   1.039   1.972  1.00  0.00           H
CONECT    4    1    2
CONECT    5    1    3
CONECT    6    1   29   30   31
CONECT    7    1   41   42   43
CONECT    8    1   32   33   34
CONECT    9    1   44   45   46
CONECT   10    3   23   24   25
CONECT   11    3   20   21   22
CONECT   12    2   50   51   52
CONECT   13    2   53   54   55
CONECT   14    2   35   36   37
CONECT   15    2   47   48   49
CONECT   16    2   38   39   40
CONECT   17    3   26   27   28
CONECT   18    3   59   60   61
CONECT   19    3   56   57   58
CONECT   20   11
CONECT   21   11
CONECT   22   11
CONECT   23   10
CONECT   24   10
CONECT   25   10
CONECT   26   17
CONECT   27   17
CONECT   28   17
CONECT   29    6
CONECT   30    6
CONECT   31    6
CONECT   32    8
CONECT   33    8
CONECT   34    8
CONECT   35   14
CONECT   36   14
CONECT   37   14
CONECT   38   16
CONECT   39   16
CONECT   40   16
CONECT   41    7
CONECT   42    7
CONECT   43    7
CONECT   44    9
CONECT   45    9
CONECT   46    9
CONECT   47   15
CONECT   48   15
CONECT   49   15
CONECT   50   12
CONECT   51   12
CONECT   52   12
CONECT   53   13
CONECT   54   13
CONECT   55   13
CONECT   56   19
CONECT   57   19
CONECT   58   19
CONECT   59   18
CONECT   60   18
CONECT   61   18
ENDMDL
END
• 1 views • link
written by dimkal dimkal

thanks a lot. I think u have generated this using Ligprep in maestro. However our institute haven't purchased maestro. though it will help me in having an idea about the 3D strc but still need to find out free tools for converting 2D to 3D.

• 0 views • link
written by Tofayel Ahmed • Tofayel Ahmed

u can use chemsketch(freely available) to draw the structure and further do its 3D optimization and then save file in MDL(V2000) format then with help of open babel(free) u can convert it into pdb.

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written by contactmemanishas • contactmemanishas

Actually I downloaded the mol file from the website and converted it to pdb with Maestro. I tried converting SMILES string (from wikipedia page) to 3d structures using LigPrep and the it failed due to unknown Ruthenium atom type (Schrodinger tools are developed to work with organic materials only, for now).

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written by dimkal dimkal

hello You can use the program chembiooffice,it is easy to do this.

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written by Southwan • Southwan

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