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Molecule News and Molecule of the Day
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The molecule of the day is: AZT
AZT has saved many AIDS patients. When used in a cocktail of
anti-viral agents, it is highly effective against HIV, human
immuno-deficiency virus. As shown at right, it has a remarkable
structure, with a long straight nitrogen side chain, which is thought to
assist its transition through cell membranes and other tissues, so that
it can permeate deeply into the infected areas. It is a reverse
transcriptase inhibitor, which is apparent from its thymidine-like
structure, and which means that it can interfere with the life
cycle of the virus by blocking the generation of viral DNA.
AZT is truly an amazing molecule. It does have many
unhealtful side effects, but it is effective against a devasting disease,
which was at one time mostly fatal, although I think that it indicates
the caution with which we should approach nucleic acid analogs in
general, which includes such commonplace molecules as caffeine.
AZT related molecules gallery and structural archive
3'-Azido-3'-deoxythymidine 30516-87-1 AZT C07210 Zidovudine
related molecule names:
e 3'-Azido-3'-deoxythymidine 30516-87-1 399024-19-2 AZT Azidothymidine BW A509U
BW-A 509U CCRIS 105 Combivir Compound S DRG-0004 HSDB 6515 NSC 602670 Retrovir
Thymidine, 3'-azido-3'-deoxy- Trizivir ZDV ZIDOVUDINE Zidovudina [Spanish]
Zidovudine [USAN:BAN:INN:JAN] Zidovudinum [Latin]
5'-triphosphate 3'-Deoxy-3'-azidothymidine triphosphate 92586-35-1 AZT
triphosphate Azt-TP Dttp(3'N3) Erythro-azt-TP Threo-azt-TP Thymidine
5'-(tetrahydrogen triphosphate), 3'-azido-3'-deoxy-
AIDS-122346 AIDS122346 AZT ANALOGS AZT-Leu
AIDS-122347 AIDS122347 AZT ANALOGS AZT-iLeu
AIDS-122348 AIDS122348 AZT ANALOGS AZT-Val
AIDS-122349 AIDS122349 AZT ANALOGS AZT-Ac Oxalic acid
3'-Azido-3'-deoxythymidine 3'-Azidothymidine 3'-Deoxy-3'-azidothymidine
30516-87-1 AZT Azidothymidine Azitidin BW-A 509U NSC602670 Retrovir
Thymidine,3'-azido-3'-deoxy- Timazid ZDV Zidovudine
30516-87-1 AIDS-000001 AIDS000001 AZT Azidothymidine BW A509U NSC602670
Retrovir Thymidine, 3'-azido-3'-deoxy- ZDV Zidovudine
AIDS-000044 AIDS000044 AZT Prodrug AZT-DHP DP-AZT HPAZT Thymidine,
116333-42-7 (IODIDE SALT)
AIDS000045 AZT Nicotinate methiodide AZT-DHP (*Quaternary salt*) AZT-DHP QS
Thymidine, 3'-azido-3'-deoxy-, 5'-ester with 3-carboxy-1-methylpyridinium
116333-43-8 3-Nicotinyl-AZT 5'-(3-Pyridinylcarbonyl)-3'-azido-3'-deoxythymidine
AIDS-000046 AIDS000046 AZT Nicotinate
AIDS-000364 AIDS000364 AZT (threo) AzddXyloT NSC602670
AIDS-000433 AIDS000433 Foscarnet & AZT PFA & AZT Phosphinecarboxylic acid,
dihydroxy-, oxide & Thymidine, 3'-azido-3'-deoxy- Phosphonoformate &
3'-Azido-3'-deoxythymidine & Castanospermine AIDS-000448 AIDS000448 AZT &
Castanospermine CAS & AZT
AIDS-000469 AIDS000469 AZT & Probenecid
AIDS-000592 AIDS000592 Beta interferon(rIFN-beta seron) &
3'-Azido-3'-deoxythymidine(AZT) rIFN-beta seron & AZT
3'-Azido-2',3'-dideoxythymidine & sCD4(soluble recombinant protein) AIDS-000596
AIDS000596 AZT & rsT4 AZT & sCD4 AZT & srCD4
.alpha.-D-Tocopherol acid succinate & AZT AIDS-000670 AIDS000670 ATS & AZT
H-1-benzopyran-6-yl] ester & AZT
6'-.alpha.-Fluorocarbocyclic AZT AIDS-000679 AIDS000679 F-carbocyclic-AZT
]tetrakis-ethanol & 3'-Azido-3'-deoxythymidine AIDS-000718 AIDS000718 DPM & AZT
Dipyridamole & AZT Persantin & AZT Thymidine, 3'-azido-3'-deoxy- &
128008-46-8 5'-Thymidylic acid, 3'-azido-3'-deoxy-,
mono[2,3-bis[(1-oxotetradecyl)oxy]propyl] ester, (R)- AIDS-000727 AIDS000727
Dimyristoylphosphatidyl AZT (liposomal formulation) Phosphatidyl AZT
128028-70-6 AIDS-000728 AIDS000728 AZT Diphosphate dipalmitoylglycerol
(liposomal formulation) AZTdpdg Thymidine 5'-(trihydrogen diphosphate),
3'-azido-3'-deoxy-, P'-[2,3-bis[(1-oxohexadecyl)oxy]propyl] ester, (R)-
125780-97-4 3'-Azido-3'-deoxythymidine-retinoic acid ester AIDS-000743
AIDS000743 AZT Prodrug Retinoic acid analog Retinoyl-AZT
(3b,20b)-20-carboxy-11-oxo-30-norolean-12-en-3-yl 2-O-b-D-glucopyranuronosyl- &
Thymidine, 3'-azido-3'-deoxy- 30-Noroleanane & AZT AIDS-000756 AIDS000756
Glycyrrhizin & 3'-Azido-3'-deoxythymidine Glycyrrhizin & AZT Potenlini & AZT
3'-Azido-3'-deoxythymidine & Dextran sulfate AIDS-000758 AIDS000758 AZT &
Dextran sulfate (DS)
3'- Azido-3'-deoxythymidine & Granulocyte-macrophage colony-stimulating factor
AIDS-000759 AIDS000759 AZT & Colony-stimulating factor 2 AZT & GM-CSF
3'-Azido-3'deoxythymidine & Interferon .alpha. AIDS-000760 AIDS000760 AZT &
1-.beta.-D-Ribofuranosyl-1,2,4-triazolo-3-carboxamide(Ribavirin) & Thymidine,
3'-azido-3'-deoxy- AIDS-000762 AIDS000762 Ribavirin & AZT Ribavirin & ZDV
3'-Azido-3'-deoxythymidine & Ansamycin AIDS-000766 AIDS000766 AZT & Ansamycin
Thymidine, 3'-azido-3'-deoxy- &
2-amino-1,9-dihydro-9-[(2-hydroxyethoxy)methyl]- & Thymidine,
3'-azido-3'-deoxy- ACV & AZT AIDS-000767 AIDS000767
2',3'-Dideoxycytidine & 3'-Azido-3'-deoxythymidine AIDS-000768 AIDS000768
Cytidine, 2',3'-dideoxy- & Thymidine, 3'-azido-3'-deoxy- ZDV & ddC ddC & AZT
AIDS-000769 AIDS000769 Inosine & AZT & Isoprinosine Inosine-Pranobex Inpx
Thymidine, 3'-azido-3'-deoxy- & Benzoic acid, 4-(acetylamino)- with 2-Propanol,
nyl]methyl]- & Thymidine, 3'-azido-3'-deoxy-
3'-Azido-3'-deoxythymidine AIDS-000770 AIDS000770 Avarol & AZT
1-.beta.-D-Ribofuranosyluracil & Thymidine, 3'-azido-3'-deoxy- AIDS-000771
AIDS000771 Uridine & 3'-Azido-3'-deoxythymidine Uridine & AZT
3'-Azido-3'-deoxythymidine & 9-(1,3-Dihydroxy-2-propoxymethyl)guanine
AIDS-000772 AIDS000772 AZT & DHPG AZT & Ganciclovir Thymidine,
3'-azido-3'-deoxy- & Guanine, 9-((2-hydroxy-1-(hydroxymethyl)ethoxy)methyl)-
5'-IIIIIIIIIIIII-3' and 3'-CCCCCCCCCCCCU-5' AIDS-000776 AIDS000776 Ampligen &
3'-Azido-3'-deoxythymidine Ampligen & AZT Ampligen & Thymidine,
3'-Azido-3'-deoxythymidine & 9-(2-phosphonylmethoxyethyl)adenine AIDS-000777
AIDS000777 AZT & PMEA Adefovir & AZT Thymidine, 3'-azido-3'-deoxy- & Phosphonic
3'-Azido-3'-deoxythymidine & 6-Thiodeazaguanine 52605-85-3 AIDS-000782
AIDS000782 AZT & 6-Thiodeazaguanine Thymidine, 3'-azido-3'-deoxy- &
3'-Azido-3'-deoxythymidine & N-Butyl-deoxynojirimycin AIDS-000784 AIDS000784
AZT & N-Butyl-DNJ Thymidine, 3'-azido-3'-deoxy- & 3,4,5-Piperidinetriol,
biphenyl selenium stylized
arginine highway stylized
infinite carbon chain stylized
Cysteine with hydrogens
RSS News Feed
updated Wed Sep 17 23:56:32 EDT 2008
Added Molscript graphics and MOD desktop image to the right sidebar. The theme is infinite carbon chain. The code is in infrastructure. The other main molecular graphics programs in use at this time are RasMol, Rester3D, PyMOL, and PovChem. The viewer is xzgv, and ImageMagick for touch up; mainly mogrify and convert. Please feel free to send any questions along.
updated Thu Sep 11 22:33:51 EDT 2008
We continue to get encouragment to provide coordinate files
with improved geometry, although this is a computationally
intensive task which is down the road still. Meanwhile,
a few supurb 3-dimensional structures are already found in the
archive, and two of them have been featured in the right
sidebar today. If you rummage around in the MOD galleries, you
are likely to find more 3D coordinate files, as well as
some very interesting 2D representations! In our opinion,
many of the most interesting molecules have planar geometry,
so that the current files are quite useful. In due course,
we plan to provide a comprehensive collection of coordinate
files with good stereochemical geometry, all in the selfsame
spirit of free and open source software and public access.
We welcome any and all input.
updated Wed Sep 10 20:28:49 EDT 2008
Our new directory style was featured in a the right sidebar of the Jasmone MOD page today. Just click
the directory link from the top page or in any of the recent galleries to view this new feature. These
pages typically include links to the source databases, which often have chemical diagrams or useful additional
information about the molecules. A smiley code is currently featured at the bottom of each page. Smile.
updated Thu Sep 4 22:28:57 EDT 2008
Added quick navigation links to the left side bar. The site has reached 111 GB, and a massive backup is underway. We are
still just getting started.
updated Thu Sep 4 13:30:20 EDT 2008
Added developer links to the left side bar.
updated Wed Sep 3 12:05:13 EDT 2008
I have automated the process to make molecule galleries, which I am finding very useful to my research, so I thought that I would share the opportunity and take requests. It is quick and easy. I did a bisphenol search today, and as I expected, the search turned up a few stilbenes, which is the same molecular family as resveratrol. Strikingly, Bisphenol A is a noted teratogen, which shows that care must be taken when using such molecules during pregnancy, nursing, and development. Here is a link to the bisphenol gallery.
If you would find it useful, I am definitely interested in taking requests for molecule galleries. Just send me the name of your favorite molecule. As you may be able to tell, we have access for galleries to about 1% or 0.5 million structures, in the total archive thus far, but it is already quite useful. The automated jobs are underway to fill in the rest. The next milestone is the capability to index and make galleries for the remaining millions of molecules for which we have pdb files already, which would be 5-10% complete. Any comments or suggestions are also welcome.
updated Tue Sep 2 14:10:15 EDT 2008
A terminal screenshot has been added to the right sidebar,
in order to show the kind
of code that is being used to generate the Molecules directory indices. All
inquiries and suggestions are welcome.
updated Fri Aug 29 14:39:14 EDT 2008
Reaction to our website has been quite positive and encouraging, but people are anxious to
see structures with improved stereochemistry. We have received many suggestions about how
to make that happen faster. For the time being, we are experiencing the
best structure viewing results with RasMOL. Name extraction and structure file linking
jobs are underway, which is an indication that we are still in a preliminary phase. Google
spiders more almost everyday, and past experience indicates that the search capability will
become very useful indeed! Here is some secret mumbo jumbo. I'm afraid that my Japanese
or Korean is broken at best ;-}. Enjoy!
updated Wed Aug 27 21:38:32 EDT 2008
An RSS News Feed has been added to the right side bar.
updated Tue Aug 26 19:27:29 EDT 2008
Several new indices have been added to our sidebar, notably;
current index by name, and
gallery by name. These are large indices, but also
vastly incomplete, and work is underway to improve them.
A list of bloggers who have mentioned the site, with links in their blogs, is now in the front sidebar,
although only one is known thus far. Due to the vastness of the scale,
many of these things will be divided out and buried a little deeper
eventually, but they can be showcased now, and they are a good survey.
updated Tue Aug 19 19:45:09 EDT 2008
Some facts: The Molecules website contains more than
4 million small molecule structure files in pdb format,
and molecular graphics representations. About 50
million molecules are still in the pipe, and they are expected
to appear here over the course of the next few weeks and months.
The pdb format is readable by common FOSS molecule viewer software,
such as RasMol and PyMOL.
In due course, we plan to provide high quality structures via
energy minimization refinement, and additional resources.
Molecules@gnu-darwin.org is founded
in the spirit of free software, open source, and public access.
It is hoped that access to these files will be a wonderful community
resource for science education, research, and entertainment as well.
We are looking for investment, funding, or sponsorship in order to expedite and expand this work, and lead the field,
with an eye towards an advanced, complete, synthetic, structural, and informatical bioorganome.
Meanwhile, the site is already an exceptional lab resource,
and molecular catalog, providing the means and building blocks
towards additional novel structures. We aim to be the best.
The structural biology, protein crystallography, and molecular graphics talent that is
building the Molecules archive is available to work for you in
a contract or consulting arrangement. Wide-ranging expertise is available.
Molecules@gnu-darwin.org is built entirely with
free and open source
software, GNU-Darwin OS, and it is under
the aegis of
The GNU-Darwin Distribution.
Here is a link to the
Our founder is an X-ray laboratory admin for the
Department of Biophysics and Biophysical
Chemistry of Johns Hopkins University School of Medicine. You can also
read his CV.
We would like to build a community around this website, and we are looking for
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to contact us,
email@example.com, with gdmolecules in the subject line. Cheers!