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    The molecule of the day is: DNA

    The DNA molecule is the genetic basis for all known life forms, except possibly arguably certain viruses, a very small exception indeed. DNA encodes the operational instructions for the cell, largely determining protein structure and function, as well as the expression of its own gene products. Can there be a more important molecule than DNA, which contains the mystery of life in its sequence? The double helical structure of the DNA molecule was obtained by Francis Crick and James Watson, based in part on molecular modelling, and in part on the foundational experimental work of Rosalind Franklin, diffraction specialist, and brilliant scientist. It is perhaps a pity that her DNA did not contain the instructions to keep her alive long enough to receive the Nobel prize with Watson and Crick. Our archive provides many interesting representations of DNA structure, which are sometimes very complex. As in the adenine figure at right, the bases are occasionally stubbed in with light gray or purple in order to clarify the structure of the phospho-ribosyl backbone. Enjoy!

    DNA related molecules gallery and structural archive

    other names: C00821 DNA adenine

    SMILES: *

    related molecule names:
    (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m 9007-49-2 C00039 DNA DNAn DNAn+1 Deoxyribonucleic acid C00271 Single-stranded DNA C00434 Double-stranded DNA C00578 DNA 5'-phosphate C00821 DNA adenine C00856 Cytosine (in DNA) DNA cytosine Alkylated DNA C00871 5'-Phospho-DNA C02128 C02270 Depurinated DNA 5'-Dephospho-DNA C02374 C02410 Glucosylated DNA C02840 Linear DNA duplexes 5-Methylcytosine (in DNA) C02967 DNA 5-methylcytosine DNA containing 5-methylcytosine C03103 Cyclobutadipyrimidine Cyclobutadipyrimidine (in DNA) C03110 DNA N4-methylcytosine C03391 DNA 6-methylaminopurine C04250 DNA containing 6-O-methylguanine C04381 DNA 4,6-diamino-5-formamidopyrimidine 2,6-Dichlor-4-nitroanilin 2,6-Dichloro-4-nitroaniline 2,6-Dichloro-4-nitrobenzenamine 4-Nitroaniline, 2,6-dichloro- 99-30-9 AL-50 Allisan Aniline, 2,6-dichloro-4-nitro- Benzenamine, 2,6-dichloro-4-nitro- Bortran Botran CDNA CNA DCNA DCNA (fungicide) Dichloran Dichloran (amine fungicide) Dicloran Ditranil NSC218 RD-6584 Resisan U-2069 WLN: ZR BG FG DNW 151-32-6 Adimoll DN Adipic acid, dinonyl ester Bisoflex DNA Di-n-nonyl adipate Dinonyl adipate Hexanedioic acid, dinonyl ester NSC11041 Plastomoll Na 2,4-Dinitro-6-(1-methylbutyl)phenol 2-(1-Methyl-n-butyl)-4,6-dinitrophenol 2-(1-Methylbutyl)-4,6-dinitrofenol 2-(1-Metil-butil)-4,6-dinitro-fenolo 2-sec-Amyl-4,6-dinitrophenol 4,6-Dinitro-o-sec-amylphenol 4097-36-3 Chemox General DNAP DNOSAP Dinosam Dinosame NSC21493 Phenol, 2-(1-methylbutyl)-4,6-dinitro- WLN: WNR BQ ENW CY3&1 Methotrexate, mixt. with Herring Sperm DNA NSC219744 6-Mercaptopurine, mixt. with Herring Sperm DNA NSC219745 2H-1,3,2-Oxazaphosphorin-2-amine, N,N-bis(2-chloroethyl) tetrahydro-, 2-oxide, mixt. with Herring Sperm DNA NSC219746 Herring Sperm DNA, mixt. with STEPA (NSC 6396) NSC219747 Guanidine, 1,1'-[(methylethanediylidene)dinitrilo]di-, mixt. with Calf Thymus DNA NSC219748 NSC262644 PHORBOL-12-TETRADECANOYL-13-ACETATE TPA Tetradisant-[[4-(1,1-dimethylethyl)-2-methylphenyl]dithio]-, 1-oxideomega.-[2-(dodecylthio)ethoxy]-,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-, (8S-cis)-, mixt. with denatured calf thymus DNAA, (2S-cis)-, compd. with sulfinylbis[methane] (2:1)2S-cis)-1:9) Coralyne, salt with calf thymus DNA (lyophilised, sonicated, autoclaved) (1:10) NSC282680 Coralyne, salt with calf thymus DNA (Lyophilised,non- sonicated,autoclaved) (1:5) NSC282681 Coralyne, salt with calf thymus DNA (non-denatured, non-autoclaved) (1:10) NSC282682 Coralyne, salt with calf thymus DNA (lyophilised, sonicated, autoclaved) (1:5) NSC282754 1,2,3-Propanetricarboxylic acid, 2-hydroxy-, trisodium salt 2-Hydroxy-1,2,3-propanetricarboxylic acid, trisodium salt 68-04-2 8055-55-8 CCRIS 3293 Citnatin Citreme Citric acid, trisodium salt Citrosodina Citrosodine Citrosodna EINECS 200-675-3 FEMA No. 3026 HSDB 5201 Natrocitral Sodium citrate Sodium citrate (Na3C6H5O7) Sodium citrate anhydrous TRISODIUM CITRATE Trisodium 2-hydroxy-1,2,3-propanetricarboxylate Trisodium citrate, anhydrous 151-32-6 Adimoll DN Adipic acid, dinonyl ester Adipic acid, dinonyl ester (8CI) Bisoflex DNA Bisoflex dinonyl adipate DI-N-NONYL ADIPATE Dinonyl adipate EINECS 205-789-7 HSDB 5653 Hexanedioic acid, dinonyl ester NSC 11041 Plastomoll Na 11beta,16alpha,17,21-Tetrahydroxypregna-1,4-diene-3,20-dione cyclic 16,17-acetal with acetone 16-alpha-Hydroxyprednisole-16,17-acetonide 638-94-8 Apolar D 2083 D-2083 DESONIDE DesOwen Desilux Desonida [INN-Spanish] Desonide [USAN:BAN:INN] Desonidum [INN-Latin] EINECS 211-351-6 Flusemidon Hamiltoderm Locapred Otic Tridesilon Prednacinolone Prednisolone-16,17-acetonide, 16-alpha-hydroxy- Pregna-1,4-diene-3,20-dione, 11,21-dihydroxy-16,17-((1-methylethylidene)bis(oxy))-, (11beta,16alpha)- Prenacid Reticus Sterax Steroderm Topifug Tridesilon Tridesonit Zotinar 1817-73-8 2,4-Dinitro-6-bromanilin [Czech] 2,4-Dinitro-6-bromanilin (czech) 2,4-Dinitro-6-bromoanilin [Czech] 2,4-Dinitro-6-bromoaniline 2-BROMO-4,6-DINITROANILINE 2-Bromo-4,6-dinitroaminobenzene 4-12-00-01734 (Beilstein Handbook Reference) 6-Bromo-2,4-dinitroaniline Aniline, 2,4-dinitro-6-bromo- Aniline, 2-bromo-4,6-dinitro- BRN 0916722 Benzenamide, 2-bromo-4,6-dinitro- Benzenamine, 2-bromo-4,6-dinitro- Bromo DNA CCRIS 820 EINECS 217-329-2 HSDB 5453 NCI-C60844 NSC 16572 1-Amino-2-methoxy-4-oxyanthraquinone [Russian] 1-Amino-4-hydroxy-2-methoxy-9,10-anthracenedione 1-Amino-4-hydroxy-2-methoxyanthraquinone 11116-41-9 1A-2MO-4OA [Russian] 2379-90-0 9,10-Anthracenedione, 1-amino-4-hydroxy-2-methoxy- ANTHRAQUINONE, 1-AMINO-4-HYDROXY-2-METHOXY- Acetoquinone Light Pink RLZ Artisil Brilliant Pink RFS BRN 2420171 C.I. 60755 C.I. Disperse Red 4 Celliton Fast Pink RF Celliton Fast Pink RFA-CF Cerven disperzni 4 [Czech] Cilla Fast Pink RF Dianix Fast Pink R Disperse Pink Zh Disperse Rose Zh Disperse red-4 EINECS 219-170-4 Esteroquinone Light Pink RLL Fenacet Fast Pink RF Interchem Acetate Fast Pink DNA Miketon Fast Pink RL Miketon Polyester Pink RL NSC 81265 Nyloquinone Pink B Palanil Pink RF Periliton Brilliant Pink R Perliton Brilliant Pink R Samaron Pink RFL Supracet 2,4-Dinitro-6-(1-methylbutyl)phenol 2-(1-Methyl-n-butyl)-4,6-dinitrophenol 2-(1-Methylbutyl)-4,6-dinitrofenol [Dutch] 2-(1-Metil-butil)-4,6-dinitro-fenolo [Italian] 2-sec-Amyl-4,6-dinitrophenol 2-sec-Amyl-4,6-dinitrophenol (VAN) 4,6-Dinitro-o-sec-amylphenol 4097-36-3 AI3-19047 BRN 2473527 Caswell No. 388 Chemox General DNAP DNOSAP Dinosam Dinosame [French] Dinosame [French] EPA Pesticide Chemical Code 037504 NSC 21493 Phenol, 2-(1-methylbutyl)-4,6-dinitro- 20330-10-3 2H-Pyran-2,4(3H)-dione, 3-acetyl-6-methyl-, ion(1-), sodium 2H-Pyran-2,4(3H)-dione, 3-acetyl-6-methyl-, ion(1-), sodium salt 2H-Pyran-2,4(3H)-dione, 3-acetyl-6-methyl-, monosodium salt 2H-Pyran-2,4(3H)-dione, 3-acetyl-6-methyl-, sodium salt 3-(1-Hydroxyethylidene)-6-methyl-2H-pyran-2,4(3H)-dione, sodium salt 3-Acetyl-6-methyl-2H-pyran-2,4(3H)-dione sodium salt 4-Hexenoic acid, 2-acetyl-5-hydroxy-3-oxo, delta-lactone, sodium derivative 4418-26-2 56172-68-0 71756-27-9 74240-24-7 78891-90-4 CCRIS 1895 Caswell No. 278A DHA-S DHA-sodium DHN Dehydroacetic acid, sodium salt EINECS 224-580-1 EPA Pesticide Chemical Code 027802 HSDB 4236 Harven Kyselina dehydroacetova sodna sul [Czech] New Side S 01 Prevan SODIUM DEHYDROACETATE Sodium 1-(3,4-dihydro-6-methyl-2,4-dioxo-2H-pyran-3-ylidene)ethanolate Sodium 3-acetyl-6-methyl-2,4-pyrandione Sodium 3-acetyl-6-methyl-2H-pyran-2,4(3H)-dione Sodium Dehydroacetate [USAN] 5714-75-0 PREDNAZATE Prednazate [USAN:INN] (E)-3-p-Anisoyl-3-bromoacrylic acid sodium salt 2-Butenoic acid, 3-bromo-4-(4-methoxyphenyl)-4-oxo-, sodium salt, (E)- 2-Butenoic acid, 3-bromo-4-(4-methoxyphenyl)-4-oxo-, sodium salt, (E)- (9CI) 21739-91-3 ACRYLIC ACID, 3-p-ANISOYL-3-BROMO-, SODIUM SALT, (Z)- Acrylic acid, 3-p-anisoyl-3-bromo-, sodium salt, (E)- Bromebric acid, sodium salt, (E)-isomer CCRIS 189 Cytembena HSDB 4134 NCI-C50737 Sodium (E)-beta-4-methoxybenzoyl-beta-bromoacrylate Sodna sul kyseliny cis-beta-4-methoxybenzoyl-beta-bromakrylove [Czech]

    pdb file:4017.pdb
    CAS: *

    MOD screenshot

    MOD termshot

    Prized Arginine!

    directory: 587105

    Cysteine with hydrogens

    directory: 588600

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    Molecule News

    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. 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. is built entirely with FOSS, 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 Distribution résumé. 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 volunteers and collaborators to help. Regarding any aspect of the work of this site, please feel free to contact us,, with gdmolecules in the subject line. Cheers!