Talk:Oligomycin

permission to copy

The reference to our website in order to use our image of oligomycin was done without asking us, but never mind, that's OK, I permit that anyway.

Maksim Gur, webmaster of Fermentek biotechnology 213.8.7.232 07:09, 6 December 2006 (UTC)

I am convinced that the absolute configuration of oligomycin shown in this image (http://upload.wikimedia.org/wikipedia/commons/thumb/2/20/Oligomycin.png/584px-Oligomycin.png), which is often cited in journal articles, is incorrect. I refer you to recent structure elucidation studies:

Nakata, M., et al., Bull. Chem. Soc. Jpn., 68, 967-989 (1995)

&

Wagenaar, M.S., et al., J. Nat. Prod., 70, 367-371 (2007)

The previous structure which appears to be the one shown here was reported in 1972, and disagrees with the data in the sources cited above, and with my own data as well.Dr.kwan (talk) 13:02, 18 July 2008 (UTC)

I have updated the structure to match those in the two references you have provided. Thanks for noticing the discrepancy. -- Ed (Edgar181) 20:29, 18 July 2008 (UTC)

Chemical structure

The following conversation about the chemical structure of oligomycins is copied from my user talk page in case it is of interest to anyone here. -- Ed (Edgar181) 20:44, 21 April 2016 (UTC)

Extended content

Hey Edgar, I'm trying to wrap my head around the image used for Oligomycin A . The old version you uploaded looked more consistent with the Merck Index 15th Ed. minus a few stereo bonds. When looking at the ChemSpider link for the compound, the IUPAC name is different. Unfortunately if Chemspider/Merck Index is correct, this would also change the diagram of the Oligomycins that's on the page. I am unable to access the reference mentioned in the description of the diagram (1995). The references mentioned In the Merck are all prior to 1978. Kinliss (talk) 20:49, 12 April 2016 (UTC)

I'll take a look. My memory of creating those images about 8 years ago is long gone. I'll see if I can find a copy of the Nakata reference that I noted as the basis for creating them. In the mean time, can you specify which part of the molecules you think might contain an error? -- Ed (Edgar181) 20:59, 12 April 2016 (UTC)

I obtained a copy of the Nakata paper. The chemical structure images that I created match what is shown in the paper. It is possible that the chemical structures of these compounds were originally mischaracterized. The Nakata paper is over 20 years old now and maybe the structures have since been revised. I'll continue to look and see what I can learn. -- Ed (Edgar181) 12:09, 13 April 2016 (UTC)

From the Merck Index, the stereo bonds are all flipped from the wiki image. I've seen issues in the past with Merck entries. Then the IUPAC name from Chemspider is opposite from the wiki for R's and S's.
(1R,4E,5'S,6S,6'S,7R,8S,10R,11R,12S,14R,15S,16R,18E,20E,22R,25S,27R,28S,29R) (current).
(1S,4E,5'R,6R,6'R,7R,8S,10S,11S,12R,14S,15S,16S,18E,20Z,22R,27S,28R,29S) (chem spider).
After previewing, it appears that chem spider is missing the bond orientation at the 25. The structure identification from the Merck Index is refers to "C. Merienne, T. Staron, Chem. Commun. 1978, 318". Does the Nakata paper reference another paper for it's structure? Kinliss (talk) 23:00, 20 April 2016 (UTC)

Chemical Abstracts gives the structure as "Spiro[2,​26-​dioxabicyclo[23.3.1]​nonacosa-​4,​18,​20-​triene-​27,​2'-​[2H]​pyran]​-​3,​9,​13-​trione, 22-​ethyl-​3',​4',​5',​6'-​tetrahydro-​7,​11,​14,​15-​tetrahydroxy-​6'-​[(2R)​-​2-​hydroxypropyl]​-​5',​6,​8,​10,​12,​14,​16,​28,​29-​nonamethyl-​, (1R,​2'R,​4E,​5'S,​6S,​6'S,​7R,​8S,​10R,​11R,​12S,​14R,​15S,​16R,​18E,​20E,​22R,​25S,​28S,​29R)​-". This seems to match the current images and the Nakata paper, but not Merck Index and ChemSpider. I am inclined to give the greatest weight to Chemical Abstracts because it is generally authoritative and is routinely updated with structural revisions. The Nakata paper gives the following references for description of the chemical structure:

Biochem. Biophys. Res. Commun., 34, 448 (1969)

Biochem. Biophys. Res. Commun., 44, 619 (1971)

FEBS Lett., 20, 267 (1972)

J. Org. Chem., 51, 4264 (1986)

-- Ed (Edgar181) 12:12, 21 April 2016 (UTC)

This is a more recent paper regarding the structure of Oligomycin A that confirms your structure and it's stereochemical bonds.

Bioorganic & Medicinal Chemistry 21 (2013) 2918–2924

The 1971 paper you referenced I was able to find online, but it only talked about Oligomycin B and it's crystal structure. Either way, I'll notify the authors of the Merck Index to review and correct it's entry. Thanks! Kinliss (talk) 17:49, 21 April 2016 (UTC)