[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleLibrary Docking for Cannabinoid-2 Receptor Ligands.
Journal, issue, pagesJ Med Chem, Year 2026
Publish dateJul 3, 2026
AuthorsMoira M Rachman / Christos Iliopoulos-Tsoutsouvas / Michael D Sacco / Xinyu Xu / Cheng-Guo Wu / Emma Santos / Isabella S Glenn / Lu Paris / Michelle K Cahill / Suthakar Ganapathy / Tia A Tummino / Yurii S Moroz / Dmytro S Radchenko / Meri Okorie / Vivianne L Tawfik / John J Irwin / Alexandros Makriyannis / Georgios Skiniotis / Brian K Shoichet /
PubMed AbstractCannabinoid receptors are both therapeutically attractive and are interesting model systems for structure-based methods. Here we investigated topical questions in library docking using the CB2 ...Cannabinoid receptors are both therapeutically attractive and are interesting model systems for structure-based methods. Here we investigated topical questions in library docking using the CB2 receptor. While a CB1R docking campaign found potent but nonselective ligands, here subtype selective ligands were found by targeting polar residues. Hit rates and hit affinities improved with library size, but docking against active and inactive receptor states did not reliably bias toward agonists or antagonists. Cryo-EM structures of two of the new agonists superposed well on the docking predictions. Structure-based optimization led to 10- to 140-fold improvements within three series, consistent with well-behaved ligands. Hit rates with an explicit 2.6 billion molecule library resembled those of an implied 11 billion molecule library from a building-block method, supporting the latter's ability to explore this space, though higher affinities were discovered from the explicit set. Implications for future studies are considered.
External linksJ Med Chem / PubMed:42397716
MethodsEM (single particle)
Resolution2.72 - 2.94 Å
Structure data

76463

12iy

EMDB-76463, PDB-12iy:
Locally refined cryo-EM structure of human cannabinoid receptor 2 with agonist '5249
Method: EM (single particle) / Resolution: 2.94 Å

76464

12iz

EMDB-76464, PDB-12iz:
Cryo-EM structure of human cannabinoid receptor 2-Gi complex with agonist '5249
Method: EM (single particle) / Resolution: 2.72 Å

76465

12ja

EMDB-76465, PDB-12ja:
Cryo-EM structure of human cannabinoid receptor 2-Gi complex with agonist '1029
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

PDB-1db5:
HUMAN S-PLA2 IN COMPLEX WITH INDOLE 6

PDB-1db6:
SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsMEMBRANE PROTEIN / Human cannabinoid receptor 2 / CNR2 / CB2 receptor / Gi1 / Agonist-bound state / AM12435-bound complex / Active-state GPCR / Class A rhodopsin-like receptor / Cryo-electron microscopy structure

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more