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    The molecule of the day is: Alanine

    Alanine is notable as a small amino acid, which is a component of protein. Due to the small size of its single methyl side chain, it is able to pack into crevices in protein structure, so that the main chains lay close together. As a result of its smallness, the protein chain is somewhat more flexible near alanine, but not as flexible as near glycine, which has no sidechain at all.

    Alanine related molecules gallery and structural archive

    other names: 56-41-7 C00041 L-2-Aminopropionic acid L-Alanine L-alpha-Alanine

    Canonical SMILES: CC(C(=O)O)N

    related molecule names:
    50906-85-9 Atalanine C10644 51-65-0 C11217 p-Fluorophenylalanine 65929-03-5 C11221 FMLP OMe Formylmethionyl-leucyl-phenylalanine methyl ester 20874-31-1 C11341 N-Acetyl-DL-phenylalanine beta-naphthyl ester N-Acetylphenylalanine beta-naphthyl ester 10109-05-4 C11345 Triazolealanine 59880-97-6 C11596 FMLP N-Formyl-L-methionyl-L-leucyl-L-phenylalanine 3131-03-1 4-[4-(Dimethylamino)-N-methyl-L-phenylalanine]virginiamycin S1 C11615 Mikamycin B Pristinamycin IA Vernamycin B alpha 4-[N-Methyl-4-(methylamino)-L-phenylalanine]virginiamycin S1 57206-54-9 C11616 Pristinamycin IB Vernamycin B beta 2-D-Alanine-4-[4-(dimethylamino)-N-methyl-L-phenylalanine]virginiamycin S1 28979-74-0 C11617 Pristinamycin IC Vernamycin B gamma 2410-24-4 C12033 p-Aminophenylalanine 3-CHLORO-D-ALANINE 3-HYDROXY-L-KYNURENINE 3-hydroxy-kynurenine 606-14-4 Alanine, 3-(3-hydroxyanthraniloyl)-, L- 1115-65-7 3-SULFINOALANINE 3-Sulfino-L-alanine 3-sulphino-L-alanine L-Cysteinesulfinic acid 3-UREIDO-PROPIONATE 3-Ureidopropanoate 3-ureidopropionate N-Carbamoyl-beta-alanine beta-Ureidopropionic acid 107-95-9 3-aminopropanoate B-ALANINE beta-alanine C1 UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate- D-alanyl-D-alanine UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine C3 UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine C4 N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl- D-alanyl-D-alanine-diphosphoundecaprenol C5 N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptane- D-alanyl-D-alanine-diphosphoundecaprenol lipid intermediate I undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide C6 N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptane-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine lipid intermediate II undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)-N-acetylglucosamine 923-16-0 D-ALA-D-ALA D-alanyl-D-alanine 338-69-2 D-ALANINE (S)-alpha-amino-1H-imidazole-4-propanoic acid 7006-35-1 71-00-1 HIS L-histidine alpha-amino-4-imidazoleproprionic acid glyoxaline-5-alanine histidine 56-41-7 6898-94-8 L-alanine L-alpha-alanine alanine 3,4-dihydroxy-L-phenylalanine 59-92-7 Dopa L-DIHYDROXY-PHENYLALANINE alanine, 3-(3,4-dihydroxyphenyl)-, L- dihydroxyphenylalanine 3,3'5-Triiodo-L-thyronine 3,5,3'-L-Triiodo-L-thyronine 3,5,3'-triiodothyronine 4-(3-iodo-4-hydroxy-phenoxy)-3,5-diiodophenylalanine 6893-02-3 L-3,5,3'-Triiodothyronine L-triiodothyronine LIOTHYRONINE O-(4-hydroxy-3-iodo-phenyl)-3,5-diiodo-L-tyrosine triiodothyronine triothyrone (R)-pantothenate 79-83-4 D-pantothenic acid PANTOTHENATE beta-alanine, (R)-N-(2,4-dihydroxy-3,3-dimethyl-oxobutyl)- pantothenic acid vitamin B5 3617-44-5 63-91-2 L-phenylalanine PHE endophenyl phenylalanine 17528-72-2 4(1H)-pteridinone, 2-amino-6-(1,2-dihydroxypropyl)-5,6,7,8-tetrahydro- 5,6,7,8-erythro-tetrahydrobiopterin 5,6,7,8-tetra-H-biopterin 5,6,7,8-tetrahydrobiopterin TETRA-H-BIOPTERIN phenylalanine hydroxylase cofactor tetra-hydro-biopterin tetrahydrobiopterin UDP-ACETYLMURAMOYL-ALA UDP-N-acetylmuramoyl-L-alanine UDP-MURNAC-TETRAPEPTIDE UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate-D-alanine uridine 5'-pyrophosphoryl N-acetylmuramyl-tetrapeptide 56-41-7 C00041 L-2-Aminopropionic acid L-Alanine L-alpha-Alanine 56-45-1 C00065 L-2-Amino-3-hydroxypropionic acid L-3-Hydroxy-alanine L-Serine (S)-alpha-Amino-beta-phenylpropionic acid 63-91-2 C00079 L-Phenylalanine (S)-2-Amino-3-(p-hydroxyphenyl)propionic acid (S)-3-(p-Hydroxyphenyl)alanine 60-18-4 C00082 L-Tyrosine 107-95-9 3-Aminopropanoate 3-Aminopropionic acid C00099 beta-Alanine 338-69-2 C00133 D-2-Aminopropionic acid D-Ala D-Alanine 3-Anthraniloyl-L-alanine 343-65-7 C00328 L-Kynurenine 3,4-Dihydroxy-L-phenylalanine 3-Hydroxy-L-tyrosine 59-92-7 C00355 Dihydroxy-L-phenylalanine L-Dopa L-beta-(3,4-Dihydroxyphenyl)alanine Levodopa 13100-82-8 2-Amino-3-sulfopropionic acid 3-Sulfoalanine C00506 L-Cysteate L-Cysteic acid

    pdb file:3290.pdb
    CAS: 57-48-7

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    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

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    updated Tue Aug 26 19:27:29 EDT 2008

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    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.

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