[English] 日本語
Yorodumi
- BIRD-PRD_000204: Vancomycin -

+
Open data


ID or keywords:

Loading...

-
Basic information

EntryDatabase: Biologically Interesting Molecule Reference Dictionary (BIRD) / ID: PRD_000204
StatusStatus: REF ONLY
NameVancomycin

-
BIRD information

TypeGlycopeptide / Antibiotic
Details
  • VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE AND VANCOSAMINE. HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOUGHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER.
  • VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4.
DownloadsMolecular definition / Chemical definition / Family definition
Synonyms
  • (1S,2R,18R,22S,25R,28R,40R)-48-{[(2S,3R,4S,5S,6R)-3-{[(2S,4S,5S,6S)-4-amino-5-hydroxy-4,6-dimethyloxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-22-(carbamoylmethyl)-5,15-dichloro-2,18,32,35,37-pentahydroxy-19-[(2R)-4-methyl-2-(methylamino)pentanamido]-20,23,26,42,44-pentaoxo-7,13-dioxa-21,24,27,41,43-pentaazaoctacyclo[26.14.2.2^{3,6}.2^{14,17}.1^{8,12}.1^{29,33}.0^{10,25}.0^{34,39}]pentaconta-3,5,8(48),9,11,14,16,29(45),30,32,34(39),35,37,46,49-pentadecaene-40-carboxylic acid (DrugBank)
  • AIDS070034 (PubChem)
  • Diatracin (SciFinder)
  • EINECS 2150772-6 (PubChem)
  • HSDB3262 (PubChem)
  • K288 (Norine)
  • LS-161387 (PubChem)
  • Lopac-_001267 (PubChem)
  • Lyphocin (ABX_Guide, ChemSpider)
  • Prestwick0_000497 (PubChem)
  • Prestwick1_000497 (PubChem)
  • Prestwick2_000497 (PubChem)
  • SPBio_002314 (PubChem)
  • VANCOMYCIN (PDB)
  • Vancin (Norine)
  • Vancled (Norine)
  • Vancocin (SciFinder, KEGG, DrugBank, ABX_Guide, PubChem, ChemSpider)
  • Vancocin HCL (DrugBank)
  • Vancocin Hydrochloride (KEGG)
  • Vancocin Pulvule (ABX_Guide)
  • Vancocine (SciFinder)
  • Vancoled (DrugBank)
  • Vancomicina (PubChem, ChemSpider)
  • Vancomycin (SciFinder, KEGG, DrugBank, Norine, PubChem, ChemSpider)
  • Vancomycin HCL (DrugBank)
  • Vancomycin Hcl (ABX_Guide)
  • Vancomycin Hydrochloride (ChemBank)
  • Vancomycin Monohydrochloride (ChemBank)
  • Vancomycine (PubChem, ChemSpider)
  • Vancomycinum (PubChem, ChemSpider)
  • Vancor (DrugBank, ChemSpider)
  • vancomycin (Merck)
Annotation
  • Function: Antibacterial / Info source: KEGG
  • Function: treatment of serious infections caused by susceptible strains of (beta-lactam-resistant) methicillin-resistant staphlococci / Info source: DrugBank
  • Function: drug of last resort / Info source: DrugBank
  • Function: cell wall synthesis inhibitor (prevents addition of N-acetylmuramic acid(NAM) and N-acetylglucosamine(NAG)-peptide subunits from being added into petidoglycan matrix, a major structural component of Gram-positive cell walls) / Info source: DrugBank
  • Function: alters bacterial-cell-membrane permeability and RNA synthesis / Info source: DrugBank
  • Function: Not active in vitro against gram-negative bacilli, mycobacteria, or fungi / Info source: DrugBank
  • Function: Antibiotic / Info source: Norine
  • Function: Used in prophylaxis and treatment of infections caused by Gram-positive bacteria / Info source: Norine
  • Function: Drug of last resort / Info source: Norine
  • Function: Antibacterial / Info source: NovelAntibiotics
  • Function: treatment of bone and joint infections, pneumonia, septicemia, endocarditis, and prophylaxis / Info source: ABX_Guide
  • Function: antibacterial activity / Info source: PubChem
  • Function: inhibits cell wall assembly / Info source: PubChem
  • Function: toxic to kidneys and inner ear / Info source: PubChem
Source
External info
Familyglycopeptide antibiotic

Chloroorienticin A / Vancomycin / DESVANCOSAMINYL VANCOMYCIN ...Chloroorienticin A / Vancomycin / DESVANCOSAMINYL VANCOMYCIN / VANCOMYCIN AGLYCON / Decaplanin / Teicoplanin A2-2 beta-D-Glucopyranuronic acid / Teicoplanin Aglycone / BIRD: PRD_000211 / Balhimycin / Deglucobalhimycin / MonodeChloro- Teicoplanin A2-2 / desulfo-A47934 / teicoplanin

Related structures
  • carboxy-decarboxamido-vancomycin hydrate / CCDC: VANCMN / Reference
  • Vancomycin-N-acetyl-D-alanine-D-alanine / CCDC: COGQIY / Reference
  • Vancomycin M43A hydrate / CCDC: VADNET / Reference
  • Vancomycin dichloride acetic acid hydrate / CCDC: TUCMEJ / Reference
  • Vancomycin acetate dichloride hydrate / CCDC: TUCMEJ01 / PubMed / Reference
  • tetrakis(balhimycin) dicitrate triacetate 2-methyl-2,4-pentanediol hydrate, seqres A7 LEU*-TYR*-ASN-GLY*-GLY*-TYR*-GLY* / CCDC: NOSVOG / Reference
  • ureido-balhimycin hydrate / CCDC: HICHUW / Reference
  • Sodium N-acetyl-D-alanyl-D-alanine vancomycin 2-(4-morpholino)ethylsulfonate polyethylene glycol decahydrate, seqres C6 SER*!-ASN-GLY*-GLY*-SER*!,UND, A2 LEU-SER*!, A2 SER*!-GLY*, A2 ALA*-ALA / CCDC: LOKFOH / PubMed / Reference
  • hexakis(Vancomycin) hexakis(N-acetyl-D-alanyl-D-alanine) sulfate dioxane solvate hydrate, seqres C6 SER*!-ASN-GLY*-GLY*-SER*!,UND, A2 LEU-SER*!, A2 SER*!-GLY*, A2 ALA*-ALA / CCDC: LOKFUN / PubMed / Reference
  • hexakis(Vancomycin) hexakis(N,N'-diacetyllysyl-D-alanyl-D-lactate) hydrate, seqres C6 SER*!-ASN-GLY*-GLY*-SER*!,UND, A2 LEU-SER*!, A2 SER*!-GLY*, A2 LYS*-ALA* / CCDC: LOKGAU / PubMed / Reference
  • aqua-vancomycin-copper(ii) hemikis(sodium chloride) hydrate / CCDC: NIXMAJ / PubMed / Reference
  • bis(vancomycinium) monohydrogen phosphate sodium trichloride hydrate / CCDC: WUPWAG / Reference
  • bis(vancomycinium) N-acetyl-D-alaninate sodium trichloride tritriacontahydrate / CCDC: WUPWEK / Reference

-
Chemical information

Composition
Formula: C66H75Cl2N9O24 / Formula weight: 1449.254
OthersType: peptide-like
History
External linksUniChem / ChemSpider / Wikipedia search / Google search

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

-
Details

-
SMILES

CACTVS 3.385CN[CH](CC(C)C)C(=O)N[CH]1[CH](O)c2ccc(Oc3cc4cc(Oc5ccc(cc5Cl)[CH](O)[CH]6NC(=O)[CH](NC(=O)[CH]4NC(=O)[CH](CC(N)=O)NC1=O)c7ccc(O)c(c7)c8c(O)cc(O)cc8[CH](NC6=O)C(O)=O)c3O[CH]9O[CH](CO)[CH](O)[CH](O)[CH]9O[CH]%10C[C](C)(N)[CH](O)[CH](C)O%10)c(Cl)c2
OpenEye OEToolkits 2.0.7CC1C(C(CC(O1)OC2C(C(C(OC2Oc3c4cc5cc3Oc6ccc(cc6Cl)C(C(C(=O)NC(C(=O)NC5C(=O)NC7c8ccc(c(c8)-c9c(cc(cc9O)O)C(NC(=O)C(C(c1ccc(c(c1)Cl)O4)O)NC7=O)C(=O)O)O)CC(=O)N)NC(=O)C(CC(C)C)NC)O)CO)O)O)(C)N)O

-
SMILES CANONICAL

CACTVS 3.385CN[C@H](CC(C)C)C(=O)N[C@@H]1[C@H](O)c2ccc(Oc3cc4cc(Oc5ccc(cc5Cl)[C@@H](O)[C@@H]6NC(=O)[C@H](NC(=O)[C@@H]4NC(=O)[C@H](CC(N)=O)NC1=O)c7ccc(O)c(c7)c8c(O)cc(O)cc8[C@H](NC6=O)C(O)=O)c3O[C@@H]9O[C@H](CO)[C@@H](O)[C@H](O)[C@H]9O[C@H]%10C[C@](C)(N)[C@H](O)[C@H](C)O%10)c(Cl)c2
OpenEye OEToolkits 2.0.7C[C@H]1[C@H]([C@@](C[C@@H](O1)O[C@@H]2[C@H]([C@@H]([C@H](O[C@H]2Oc3c4cc5cc3Oc6ccc(cc6Cl)[C@H]([C@H](C(=O)N[C@H](C(=O)N[C@H]5C(=O)N[C@@H]7c8ccc(c(c8)-c9c(cc(cc9O)O)[C@H](NC(=O)[C@H]([C@@H](c1ccc(c(c1)Cl)O4)O)NC7=O)C(=O)O)O)CC(=O)N)NC(=O)[C@@H](CC(C)C)NC)O)CO)O)O)(C)N)O

-
PDB entries

+
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://pdbjlvh1.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