[English] 日本語
Yorodumi
- ChemComp-YDZ: [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

EntryDatabase: PDB chemical components / ID: YDZ
NameName: [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl- ...Name: [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate

-
Chemical information

Composition
Formula: C22H32N10O16P3S / Number of atoms: 84 / Formula weight: 817.533 / Formal charge: 1
Others

5m83

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: YDZ / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5M83
History
Create componentNov 11, 2016
Initial releaseDec 20, 2017
External linksUniChem / ChemSpider / Wikipedia search / Google search

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

-
Details

-
SMILES

CACTVS 3.385CO[CH]1[CH](O)[CH](CO[P](O)(=O)O[P](S)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)O[CH]1n5c[n+](C)c6c(O)nc(N)nc56
OpenEye OEToolkits 2.0.6C[n+]1cn(c2c1c(nc(n2)N)O)C3C(C(C(O3)COP(=O)(O)OP(=O)(OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)S)O)OC

-
SMILES CANONICAL

CACTVS 3.385CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(=O)O[P@](S)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)O[C@H]1n5c[n+](C)c6c(O)nc(N)nc56
OpenEye OEToolkits 2.0.6C[n+]1cn(c2c1c(nc(n2)N)O)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[P@](=O)(OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)S)O)OC

-
InChI

InChI 1.03InChI=1S/C22H31N10O16P3S/c1-30-7-32(18-11(30)19(36)29-22(24)28-18)21-15(42-2)13(34)9(46-21)4-44-50(39,40)48-51(41,52)47-49(37,38)43-3-8-12(33)14(35)20(45-8)31-6-27-10-16(23)25-5-26-17(10)31/h5-9,12-15,20-21,33-35H,3-4H2,1-2H3,(H7-,23,24,25,26,28,29,36,37,38,39,40,41,52)/p+1/t8-,9-,12-,13-,14-,15-,20-,21-,51+/m1/s1

-
InChIKey

InChI 1.03LVAVASOWNAXXPY-KVLYALRXSA-O

-
SYSTEMATIC NAME

OpenEye OEToolkits 2.0.6[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate

-
PDB entries

Showing all 2 items

PDB-5m83:
Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpA mRNA 5' cap analog

PDB-5m84:
Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSpA mRNA 5' cap analog

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more