X-ray structure release

In order to keep folks up-to-date with X-ray structure releases I’ll post in here whenever we update Fragalysis.

Any issues just let me know.

24 new structures now available:

Fragalysis_upload_2021-01-29.xlsx (17.7 KB)

This is an excellent idea!

Some new structures are now live on Fragalysis and there are a few things to note:

  • We are now using a different crystal form (same crystal form as immature structures (Mpro-N###) but with mature protein​)
  • This crystal form has more open crystal packing and more flexibility in loops around S3/S4 region (good for ligands targeting S4)​
  • The two dimer subunits are not identical​ and the ligand is not always bound in both
  • On Fragalysis the new structures will be labelled as P####_#A/B_LigandID (where P#### refers to the dataset and #A/B refers to the protein chain and the ligand e.g. 0A is the first ligand in chain A)

Dataset CID Site Fragalysis Link

Mpro-P0187 MAT-POS-de59a476-4 Image Isoquinoline
Mpro-P0208 EDG-MED-971238d3-4 Image Isoquinoline
Mpro-P0033 MIC-UNK-91acba05-6 Image Isoquinoline
Mpro-P0047    LON-WEI-adc59df6-47 Image Ugi

Thanks, Daren, and I certainly need to revise how I’m thinking about structural elaboration from the methyl group of PET-UNK-29afea89-2. This binding mode does bring the methyl tantalizingly close to the catalytic cysteine although I (currently) believe that it will be difficult to present a covalent warhead to it.

Apologies for the delays between updates - a challenging run at Diamond and a few technical issues/corner cases were flushed out when uploading data from the new crystal form onto Fragalysis.

There are still some gremlins lurking including proper generation of the reference cartoon and when we fix these it is likely that previous snapshots will no longer work (sorry), but hopefully the data is still useful for design purposes.

If you spot any other issues, please let us know.

Dataset Compound Code Structure Site Fragalysis
Mpro-P0008 ERI-UCB-ce40166b-17 Image Quinolone
Mpro-P0009 MAT-POS-f2460aef-1 Image Ugi
Mpro-P0010 PET-UNK-c9c1e0d8-4 Image Isoquinoline
Mpro-P0012 ALP-POS-ce760d3f-2 Image Isoquinoline
Mpro-P0016 ALP-POS-64a710fa-1 Image Isoquinoline
Mpro-P0017 ALP-POS-ce760d3f-8 Image Isoquinoline
Mpro-P0018 ERI-UCB-d6de1f3c-2 Image Isoquinoline
Mpro-P0019 PET-UNK-c9c1e0d8-3 Image Isoquinoline
Mpro-P0022 VLA-UCB-29506327-1 Image Isoquinoline
Mpro-P0026 ALP-POS-8b8a49e1-4 Image Moonshot - active site
Mpro-P0030 EDG-MED-0e5afe9d-1 Image Isoquinoline
Mpro-P0031 BEN-DND-c852c98b-10 Image Isoquinoline
Mpro-P0034 EDJ-MED-92e193ae-1 Image Isoquinoline
Mpro-P0038 EDG-MED-0e5afe9d-3 Image Isoquinoline
Mpro-P0039 EDG-MED-971238d3-5 Image Isoquinoline
Mpro-P0041 MAT-POS-090737b9-1 Image Isoquinoline
Mpro-P0045 TRY-UNI-2eddb1ff-7 Image Aminopyridine
Mpro-P0053 BRU-THA-92256091-17 Image Ugi
Mpro-P0056 RAL-THA-4aa06b95-1 Image Isoquinoline
Mpro-P0057 MAT-POS-6c284e65-1 Image Isoquinoline
Mpro-P0060 MIC-UNK-45817b9b-1 Image Isoquinoline
Mpro-P0061 RAL-THA-2d450e86-26 Image Isoquinoline
Mpro-P0063 RAL-THA-2d450e86-33 Image Isoquinoline
Mpro-P0064 RAL-THA-2d450e86-10 Image Isoquinoline
Mpro-P0065 RAL-THA-2d450e86-13 Image Isoquinoline
Mpro-P0066 RAL-THA-2d450e86-1 Image Isoquinoline
Mpro-P0068 RAL-THA-2d450e86-17 Image Isoquinoline
Mpro-P0069 RAL-THA-2d450e86-7 Image Isoquinoline
Mpro-P0075 RAL-THA-2d450e86-16 Image Isoquinoline
Mpro-P0108 RAL-THA-2d450e86-6 Image Isoquinoline
Mpro-P0111 ALP-UNI-3735e77e-2 Image Isoquinoline
Mpro-P0114 ALP-POS-869ac754-1 Image Isoquinoline
Mpro-P0121 MAT-POS-fce787c2-3 Image Isoquinoline
Mpro-P0124 BEN-DND-c852c98b-5 Image Isoquinoline
Mpro-P0125 EDG-MED-971238d3-1 Image Isoquinoline
Mpro-P0129 MAT-POS-fce787c2-5 Image Isoquinoline
Mpro-P0130 RAL-THA-05e671eb-10 Image Isoquinoline
Mpro-P0141 MAT-POS-f9802937-7 Image Isoquinoline
Mpro-P0148 EDG-MED-5d232de5-3 Image Isoquinoline
Mpro-P0160 EDG-MED-5d232de5-1 Image Isoquinoline
Mpro-P0171 EDG-MED-5d232de5-6 Image Isoquinoline
Mpro-P0179 VLA-UCB-50c39ae8-7 Image Isoquinoline
Mpro-P0186 ALP-POS-c3a96089-4 Image Isoquinoline
Mpro-P0213 MAT-POS-e69ad64a-2 Image Isoquinoline
Mpro-P0224 EDJ-MED-8c98ee63-2 Image Isoquinoline
Mpro-P0240 BEN-DND-f2e727cd-5 Image Isoquinoline
Mpro-P0243 EDJ-MED-d08626de-3 Image Isoquinoline
Mpro-P0394 LON-WEI-9739a092-9
Image Isoquinoline
Mpro-P0578 RAL-THA-4aa06b95-7 Image Isoquinoline
Mpro-P0601 EDJ-MED-e4b030d8-11 Image Isoquinoline
Mpro-P0602 EDJ-MED-37aac4bd-4 Image Isoquinoline
Mpro-P0607 MAT-POS-a13804f0-3 Image Isoquinoline
Mpro-P0626 ALP-POS-fe871b40-11 Image Isoquinoline
Mpro-P0627 MAT-POS-78e1d523-1 Image Isoquinoline
Mpro-P0661 MAT-POS-932d1078-3 Image Isoquinoline
Mpro-P0996 MAT-POS-4223bc15-30 Image Isoquinoline
Mpro-P1007 MAT-POS-4223bc15-3 Image Isoquinoline
Mpro-P1015 MAT-POS-4223bc15-2 Image Isoquinoline

There are a handful of new structures now live plus you can now inspect electron density and PanDDA event maps in Fragalysis by clicking the D button and selecting which maps you want to see (we are aware of some teething issues still but if you notice anything odd please do flag).

Dataset Compound Code Structure Fragalysis
Mpro-P0207 BEN-BAS-c2bc0d80-6
Mpro-P1090 MAT-POS-4223bc15-23 Image
Mpro-P1624 EDJ-MED-1981ceba-2 Image
Mpro-P1638 EDJ-MED-1981ceba-3 Image
Mpro-P1701 MAT-POS-8695a11f-1 Image
Mpro-P1788 MAT-POS-dc2604c4-1 Image

New structures now online:

Dataset Compound ID Structure Fragalysis
Mpro-P0025 MAT-POS-afd4d4fd-2 Image
Mpro-P0074 RAL-THA-2d450e86-12 Image
Mpro-P0091 RAL-THA-8416115c-13 Image
Mpro-P0097 MAT-POS-5d65ec79-1 Image
Mpro-P0122 RAL-THA-8416115c-5 Image
Mpro-P0126 RAL-THA-2d450e86-30 Image
Mpro-P0135 MAT-POS-de59a476-2 Image
Mpro-P0145 BRU-CON-c4e3408a-1 Image
Mpro-P0151 EDG-MED-70ae9412-2 Image
Mpro-P0153 VLA-UNK-82501c2c-1 Image
Mpro-P0154 EDG-MED-70ae9412-1 Image
Mpro-P0178 MAT-POS-fce787c2-4 Image
Mpro-P0185 MAT-POS-fce787c2-6 Image
Mpro-P0188 MAT-POS-5d65ec79-2 Image
Mpro-P0238 ALP-UNI-8e43a71e-8 Image
Mpro-P0600 ALP-UNI-3735e77e-1 Image
Mpro-P0630 MAT-POS-e9e99895-11 Image
Mpro-P0640 MAT-POS-e9e99895-2 Image
Mpro-P0642 EDG-MED-ba1ac7b9-11 Image
Mpro-P0655 MAT-POS-e9e99895-6 Image
Mpro-P0744 MAT-POS-3ccb8ef6-1 Image
Mpro-P0747 MAT-POS-e9e99895-13 Image
Mpro-P0764 LON-WEI-9739a092-6 Image
Mpro-P0765 BEN-BAS-c2bc0d80-7 Image
Mpro-P0766 EDJ-MED-9e38fd34-1 Image
Mpro-P0772 EDG-MED-ba1ac7b9-13 Image
Mpro-P0776 MAT-POS-fb82b63d-3 Image
Mpro-P0777 PET-UNK-bb7ffe78-1 Image
Mpro-P0793 EDG-MED-5d232de5-7 Image
Mpro-P0800 MAT-POS-fb82b63d-1 Image
Mpro-P0805 EDG-MED-ba1ac7b9-21 Image
Mpro-P0808 MAT-POS-dd3ad2b5-2 Image
Mpro-P0811 ALP-POS-477dc5b7-5 Image
Mpro-P0816 EDG-MED-5d232de5-8 Image
Mpro-P0906 JIN-POS-6dc588a4-6 Image
Mpro-P0925 SAM-UNK-2684b532-12 Image
Mpro-P0978 EDJ-MED-611d11e7-4 Image
Mpro-P1200 MAT-POS-e6dd326d-6 Image
Mpro-P1477 MAT-POS-a13804f0-4 Image
Mpro-P1507 MAT-POS-8293a91a-8
Mpro-P1623 EDJ-MED-1981ceba-4 Image
Mpro-P1661 EDG-MED-10fcb19e-1 Image
Mpro-P1783 EDJ-MED-6bf93aa8-1
Mpro-P1800 VLA-UCB-50c39ae8-2
Mpro-P1835 EDJ-MED-015fb6b4-2
Mpro-P1858 ALP-POS-6f6ae286-3
Mpro-P2005 ADA-UCB-6c2cb422-1 Image
Mpro-P2007 PET-UNK-8df914d1-2 Image
Mpro-P2010 MIC-UNK-08cd9c58-1 Image
Mpro-P2011 MAT-POS-bfb445d4-2 Image
1 Like
Dataset Compound ID Structure Fragalysis
Mpro-P2001 JAN-GHE-5a013bed-2
1 Like
Dataset Compound Code Structure
Mpro-P0098 MAT-POS-1f3f1a6f-1
Mpro-P0743 KAD-UNI-80f122c8-2
Mpro-P0831 MAT-POS-96f51285-5
Mpro-P0845 ALP-POS-9c80c481-1
Mpro-P0850 ALP-UNI-8d415491-3
Mpro-P0851 MAT-POS-dd3ad2b5-3
Mpro-P0872 ALP-UNI-8d415491-6
Mpro-P0878 EDJ-MED-2f867453-1
Mpro-P0884 ALP-UNI-8d415491-1
Mpro-P0887 RUB-POS-1325a9ea-4
Mpro-P0904 EDG-MED-ba1ac7b9-19
Mpro-P1073 MAT-POS-e6dd326d-8
Mpro-P1202 MAT-POS-4223bc15-28
Mpro-P1470 RUB-POS-1325a9ea-14
Mpro-P1879 MAT-POS-5cd9ea36-15
Mpro-P1889 MAT-POS-5cd9ea36-13
Mpro-P1982 MAT-POS-af1eef35-2
Mpro-P1983 EDJ-MED-4fff0a85-3
Mpro-P1986 EDJ-MED-76744c27-4 Image
Mpro-P1988 EDJ-MED-4fff0a85-1 Image
Mpro-P1990 MAT-POS-5cd9ea36-21 Image
Mpro-P1991 MAT-POS-5cd9ea36-16 Image
Mpro-P2017 MAT-POS-4223bc15-12 Image
1 Like
Dataset Compound ID Structure
Mpro-P0143 VLA-UCB-34f3ed0c-11
Mpro-P0950 ALP-POS-e0fe77e5-13
Mpro-P2113 MAT-POS-1bed62cf-3
Mpro-P2222 EDJ-MED-8bb691af-4
1 Like
Dataset Compound Code Structure
Mpro-P1010 MAT-POS-4223bc15-18
Mpro-P1079 MAT-POS-4223bc15-40
Mpro-P1980 MAT-POS-5cd9ea36-18
Mpro-P1981 PET-UNK-b38839dc-1
Mpro-P2028 ALP-POS-6479a3a9-2
Mpro-P2036 ALP-POS-1cbc2fae-1
Mpro-P2067 MAT-POS-5cd9ea36-14
Mpro-P2178 MAT-POS-e119ab4f-3
Mpro-P2182 MAT-POS-e119ab4f-2
Mpro-P2183 MAT-POS-90fd5f68-37
Mpro-P2218 MAT-POS-90fd5f68-19 Image
Mpro-P2219 MAT-POS-90fd5f68-22
Mpro-P2224 MAT-POS-e119ab4f-1 Image
Mpro-P2229 MAT-POS-90fd5f68-21 Image
Mpro-P2256 EDJ-MED-43f8f7d6-6 Image
Mpro-P2284 PET-UNK-7fb4f80a-1 Image
Mpro-P2381 ALP-POS-1cbc2fae-2 Image
Mpro-P2385 MAT-POS-c7726e07-5 Image
Mpro-P2402 EDJ-MED-12c4873b-2 Image
Mpro-P2415 ALP-POS-4483ae88-4 Image
Mpro-P2468 EDG-MED-ee636701-1 Image
Dataset Compound Code Structure
Mpro-P1474 MAT-POS-afb6844f-1 Image
Mpro-P1812 MAT-POS-86c60949-2
Mpro-P1978 MAT-POS-5cd9ea36-22
Mpro-P2031 MAT-POS-a54ce14d-2
Mpro-P2039 MAT-POS-2e8b2191-11
Mpro-P2057 MAT-POS-5cd9ea36-23
Mpro-P2070 MAT-POS-bfd29aac-1
Mpro-P2072 MAT-POS-2e8b2191-10
Mpro-P2074 MAT-POS-2e8b2191-12
Mpro-P2075 MAT-POS-c20a539d-4
Mpro-P2080 ALP-POS-6f6ae286-5
Mpro-P2089 MAT-POS-5cd9ea36-2
Mpro-P2090 EDJ-MED-7889e8da-5
Mpro-P2099 ALP-POS-a577c8a2-1
Mpro-P2101 EDJ-MED-7889e8da-3
Mpro-P2141 MAT-POS-7174c657-6
Mpro-P2144 MAT-POS-90fd5f68-31
Mpro-P2176 MAT-POS-7174c657-5
Mpro-P2177 MAT-POS-90fd5f68-38
Mpro-P2185 MAT-POS-90fd5f68-2
Mpro-P2197 ALP-POS-477dc5b7-4
Mpro-P2201 PET-UNK-d899bab6-1
Mpro-P2203 MAT-POS-90fd5f68-28
Mpro-P2204 MAT-POS-90fd5f68-20
Mpro-P2205 MAT-POS-90fd5f68-14
Mpro-P2206 EDJ-MED-12c4873b-5
Mpro-P2207 MAT-POS-90fd5f68-7
Mpro-P2210 MAT-POS-90fd5f68-13
Mpro-P2214 PET-UNK-7fb4f80a-2
Mpro-P2215 EDJ-MED-be9e6f63-3
Mpro-P2242 EDJ-MED-e69ed63d-13
Mpro-P2243 EDJ-MED-c3ea9889-6
Mpro-P2263 EDJ-MED-8bb691af-6
Mpro-P2273 EDJ-MED-e69ed63d-1
Mpro-P2291 EDJ-MED-43f8f7d6-4
Mpro-P2295 EDJ-MED-968bafd9-1
Mpro-P2487 EDJ-MED-8bb691af-8
Mpro-P2601 MIK-UNK-78dbf1b8-1
Mpro-P2605 MIK-ENA-5d9157e9-6
Mpro-P2606 MIK-ENA-5d9157e9-5
Mpro-P2607 EDJ-MED-705e09b8-1
Mpro-P2649 MAT-POS-853c0ffa-9
Mpro-P2660 EDG-MED-b1ef7fe3-1
Dataset Compound Code Structure
Mpro-P2724 EDJ-MED-976a33d5-1 Image
Mpro-P2730 ALP-POS-ecbed2ba-12
Mpro-P3038 MAT-POS-e48723dc-2
Mpro-P3050 MAT-POS-50a80394-1
Mpro-P3054 MAT-POS-50a80394-2
Mpro-P3074 ALP-POS-133e7cd9-2