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cyclo[DL-Aoda-DL-Trp(OMe)-DL-xiIle-DL-Pip]

PubChem CID
21922507
Structure
cyclo[DL-Aoda-DL-Trp(OMe)-DL-xiIle-DL-Pip]_small.png
cyclo[DL-Aoda-DL-Trp(OMe)-DL-xiIle-DL-Pip]_3D_Structure.png
Molecular Formula
Synonyms
  • apicidin
  • SCHEMBL8093982
  • BCP13245
Molecular Weight
623.8 g/mol
Computed by PubChem 2.1 (PubChem release 2021.05.07)
Dates
  • Create:
    2007-12-05
  • Modify:
    2025-01-11

1 Structures

1.1 2D Structure

Chemical Structure Depiction
cyclo[DL-Aoda-DL-Trp(OMe)-DL-xiIle-DL-Pip].png

1.2 3D Conformer

2 Biologic Description

SVG Image
SVG Image
IUPAC Condensed
cyclo[DL-Aoda-DL-Trp(OMe)-DL-xiIle-DL-Pip]
HELM
PEPTIDE1{[*C(=O)C(CCCCCC(=O)CC)N* |$_R2;;;;;;;;;;;;;;_R1$|].[*C(=O)C(Cc1cn(c2c1cccc2)OC)N* |$_R2;;;;;;;;;;;;;;;;;_R1$|].[*C(=O)C(C(C)CC)N* |$_R2;;;;;;;;;_R1$|].[*C(=O)C1CCCCN1* |$_R2;;;;;;;;;_R1$|]}$PEPTIDE1,PEPTIDE1,4:R2-1:R1$$$
IUPAC
cyclo[(2-amino-8-oxodecanoyl)-N1-methoxy-DL-tryptophyl-DL-isoleucyl-DL-homoprolyl]

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

3-butan-2-yl-6-[(1-methoxyindol-3-yl)methyl]-9-(6-oxooctyl)-1,4,7,10-tetrazabicyclo[10.4.0]hexadecane-2,5,8,11-tetrone
Computed by Lexichem TK 2.7.0 (PubChem release 2021.05.07)

3.1.2 InChI

InChI=1S/C34H49N5O6/c1-5-22(3)30-34(44)38-19-13-12-18-29(38)33(43)35-26(16-9-7-8-14-24(40)6-2)31(41)36-27(32(42)37-30)20-23-21-39(45-4)28-17-11-10-15-25(23)28/h10-11,15,17,21-22,26-27,29-30H,5-9,12-14,16,18-20H2,1-4H3,(H,35,43)(H,36,41)(H,37,42)
Computed by InChI 1.0.6 (PubChem release 2021.05.07)

3.1.3 InChIKey

JWOGUUIOCYMBPV-UHFFFAOYSA-N
Computed by InChI 1.0.6 (PubChem release 2021.05.07)

3.1.4 SMILES

CCC(C)C1C(=O)N2CCCCC2C(=O)NC(C(=O)NC(C(=O)N1)CC3=CN(C4=CC=CC=C43)OC)CCCCCC(=O)CC
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C34H49N5O6
Computed by PubChem 2.1 (PubChem release 2021.05.07)

3.3 Other Identifiers

3.3.1 CAS

183506-66-3

3.3.2 European Community (EC) Number

3.3.3 HMDB ID

3.3.4 Metabolomics Workbench ID

3.3.5 Pharos Ligand ID

3.3.6 Wikidata

3.3.7 Wikipedia

3.4 Synonyms

3.4.1 MeSH Entry Terms

  • apicidin
  • apicidin C
  • cyclo(N-O-methyl-tryptophyl-isoleucyl-pipecolinyl-2-amino-8-oxodecanoyl)

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
623.8 g/mol
Reference
Computed by PubChem 2.1 (PubChem release 2021.05.07)
Property Name
XLogP3-AA
Property Value
4.4
Reference
Computed by XLogP3 3.0 (PubChem release 2021.05.07)
Property Name
Hydrogen Bond Donor Count
Property Value
3
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.05.07)
Property Name
Hydrogen Bond Acceptor Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.05.07)
Property Name
Rotatable Bond Count
Property Value
12
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.05.07)
Property Name
Exact Mass
Property Value
623.36828430 Da
Reference
Computed by PubChem 2.1 (PubChem release 2021.05.07)
Property Name
Monoisotopic Mass
Property Value
623.36828430 Da
Reference
Computed by PubChem 2.1 (PubChem release 2021.05.07)
Property Name
Topological Polar Surface Area
Property Value
139 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.05.07)
Property Name
Heavy Atom Count
Property Value
45
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
1050
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.05.07)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
5
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2019.01.04)

5 Spectral Information

5.1 Mass Spectrometry

5.1.1 LC-MS

1 of 5
View All
Authors
Laurent Debrauwer, Emilien L. Jamin, Research Centre in Food Toxicology (TOXALIM), INRAE, MetaboHUB-Metatoul platform, Toulouse, France
Instrument
LTQ Orbitrap XL Thermo Scientific
Instrument Type
LC-ESI-ITFT
MS Level
MS2
Ionization Mode
NEGATIVE
Ionization
ESI
Collision Energy
20 % (nominal)
Fragmentation Mode
HCD
Column Name
Hypersil GOLD C18 1.9 um 100 x 2.1 mm Thermo Fisher Scientific
Retention Time
23.340 min
Precursor m/z
622.361
Precursor Adduct
[M-H]-
Top 5 Peaks
199.2442 999
Thumbnail
Thumbnail
License
CC0
2 of 5
View All
Authors
Laurent Debrauwer, Emilien L. Jamin, Research Centre in Food Toxicology (TOXALIM), INRAE, MetaboHUB-Metatoul platform, Toulouse, France
Instrument
LTQ Orbitrap XL Thermo Scientific
Instrument Type
LC-ESI-ITFT
MS Level
MS2
Ionization Mode
NEGATIVE
Ionization
ESI
Collision Energy
30 % (nominal)
Fragmentation Mode
HCD
Column Name
Hypersil GOLD C18 1.9 um 100 x 2.1 mm Thermo Fisher Scientific
Retention Time
23.340 min
Precursor m/z
622.361
Precursor Adduct
[M-H]-
Top 5 Peaks

462.2852 999

199.2433 934

477.2248 628

Thumbnail
Thumbnail
License
CC0

7 Chemical Vendors

8 Pharmacology and Biochemistry

8.1 MeSH Pharmacological Classification

Histone Deacetylase Inhibitors
Compounds that inhibit HISTONE DEACETYLASES. This class of drugs may influence gene expression by increasing the level of acetylated HISTONES in specific CHROMATIN domains. (See all compounds classified as Histone Deacetylase Inhibitors.)

9 Safety and Hazards

9.1 Hazards Identification

9.1.1 GHS Classification

Pictogram(s)
Acute Toxic
Signal
Danger
GHS Hazard Statements

H300+H310+H330 (40.6%): Fatal if swallowed, in contact with skin or if inhaled [Danger Acute toxicity, oral; acute toxicity, dermal; acute toxicity, inhalation]

H300 (100%): Fatal if swallowed [Danger Acute toxicity, oral]

H310 (100%): Fatal in contact with skin [Danger Acute toxicity, dermal]

H330 (100%): Fatal if inhaled [Danger Acute toxicity, inhalation]

Precautionary Statement Codes

P260, P262, P264, P270, P271, P280, P284, P301+P316, P302+P352, P304+P340, P316, P320, P321, P330, P361+P364, P403+P233, P405, and P501

(The corresponding statement to each P-code can be found at the GHS Classification page.)

ECHA C&L Notifications Summary

Aggregated GHS information provided per 69 reports by companies from 4 notifications to the ECHA C&L Inventory. Each notification may be associated with multiple companies.

Information may vary between notifications depending on impurities, additives, and other factors. The percentage value in parenthesis indicates the notified classification ratio from companies that provide hazard codes. Only hazard codes with percentage values above 10% are shown.

9.1.2 Hazard Classes and Categories

Acute Tox. 2 (100%)

Acute Tox. 2 (100%)

Acute Tox. 2 (100%)

10 Literature

10.1 Consolidated References

10.2 NLM Curated PubMed Citations

10.3 Chemical Co-Occurrences in Literature

10.4 Chemical-Gene Co-Occurrences in Literature

10.5 Chemical-Disease Co-Occurrences in Literature

11 Patents

11.1 Depositor-Supplied Patent Identifiers

11.2 WIPO PATENTSCOPE

12 Classification

12.1 MeSH Tree

12.2 UN GHS Classification

13 Information Sources

  1. European Chemicals Agency (ECHA)
    LICENSE
    Use of the information, documents and data from the ECHA website is subject to the terms and conditions of this Legal Notice, and subject to other binding limitations provided for under applicable law, the information, documents and data made available on the ECHA website may be reproduced, distributed and/or used, totally or in part, for non-commercial purposes provided that ECHA is acknowledged as the source: "Source: European Chemicals Agency, http://echa.europa.eu/". Such acknowledgement must be included in each copy of the material. ECHA permits and encourages organisations and individuals to create links to the ECHA website under the following cumulative conditions: Links can only be made to webpages that provide a link to the Legal Notice page.
    https://echa.europa.eu/web/guest/legal-notice
  2. Human Metabolome Database (HMDB)
    LICENSE
    HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.
    http://www.hmdb.ca/citing
  3. MassBank Europe
  4. Metabolomics Workbench
  5. Pharos
    LICENSE
    Data accessed from Pharos and TCRD is publicly available from the primary sources listed above. Please respect their individual licenses regarding proper use and redistribution.
    https://pharos.nih.gov/about
  6. Wikidata
    cyclo[DL-Aoda-DL-Trp(OMe)-DL-xiIle-DL-Pip]
    https://www.wikidata.org/wiki/Q104169937
  7. Wikipedia
  8. PubChem
  9. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
    Histone Deacetylase Inhibitors
    https://www.ncbi.nlm.nih.gov/mesh/68056572
  10. GHS Classification (UNECE)
  11. PATENTSCOPE (WIPO)
CONTENTS