tag:blogger.com,1999:blog-1136153439451224584.post9093334807299097094..comments2024-03-27T06:45:59.174-07:00Comments on Practical Fragments: Poll: how many atoms are too few?Dr. Teddy Zhttp://www.blogger.com/profile/07288045760981372367noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-1136153439451224584.post-80951047270459894892013-04-24T20:17:16.482-07:002013-04-24T20:17:16.482-07:00Blogger is behaving like all too many governments ...Blogger is behaving like all too many governments and "losing" votes, so we've switched to Polldaddy. Apologies to those of you who voted on April 23 - please vote again.Dan Erlansonhttps://www.blogger.com/profile/07927082337051189270noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-37677936567387662252013-04-24T04:17:07.997-07:002013-04-24T04:17:07.997-07:00But hydrogen bonds are stronger than van der Waals...But hydrogen bonds are stronger than van der Waals forces. Even though binding sites don't like water and will give you free energy to displace it I would still expect an oxygen or nitrogen (or halide for that matter) to contribute more to the binding affinity than a carbon.Morten Grøftehaugehttps://www.blogger.com/profile/05252471246488393284noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-88885829516797640652013-04-23T07:39:33.451-07:002013-04-23T07:39:33.451-07:00Yes
Yes<br />Dr. Teddy Zhttps://www.blogger.com/profile/07288045760981372367noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-73863058479337928412013-04-23T07:32:39.576-07:002013-04-23T07:32:39.576-07:00Just to be clear here, you're talking about th...Just to be clear here, you're talking about the number of non-hydrogen atoms (heavy atoms), right?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-41484545871005489482013-04-23T07:30:13.111-07:002013-04-23T07:30:13.111-07:00Great poll. My thoughts which I will share while ...Great poll. My thoughts which I will share while polling is active is "9-10" in your general library. Why, you ask? For a good LEAN compound (>0.3) with 10 heavy atoms, it has a KD of 1mM. 9 HAC gives you ~2mM. Going to 8 HAC gives you 4mM. While there are methods that can robustly detect these, I would hope that you find something with significantly better affinity. For example, 12 HAC with 0.3LEAN gets you into the 200 or so uM range. Dr. Teddy Zhttps://www.blogger.com/profile/07288045760981372367noreply@blogger.com