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Oblimersen

PubChem CID
118984458
Structure
Oblimersen_small.png
Molecular Formula
Synonyms
  • oblimersen
  • Genasense
  • G3139
  • DNA, d(P-thio)(T-C-T-C-C-C-A-G-C-G-T-G-C-G-C-C-A-T)
  • GTPL8269
Molecular Weight
5685 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2016-04-10
  • Modify:
    2025-01-18
Description
Oblimersen is a phosphorothioate antisense oligonucleotide. Targeted to the initiation codon region of the bcl-2 mRNA, oblimersen inhibits bcl-2 mRNA translation, resulting in decreased expression of the bcl-2 protein, an apoptotic inhibitor expressed in some types of cancer and linked to tumor drug resistance. This agent may enhance the efficacy of standard cytotoxic chemotherapy. (NCI04)

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Oblimersen.png

1.2 3D Status

Conformer generation is disallowed since too many atoms, too flexible

2 Biologic Description

IUPAC Condensed
dThd-sP-dCyd-sP-dThd-sP-dCyd-sP-dCyd-sP-dCyd-sP-dAdo-sP-dGuo-sP-dCyd-sP-dGuo-sP-dThd-sP-dGuo-sP-dCyd-sP-dGuo-sP-dCyd-sP-dCyd-sP-dAdo-sP-dThd
Sequence
TCTCCCAGCGTGCGCCAT
HELM
RNA1{[dR](T).[sp][dR](C).[sp][dR](T).[sp][dR](C).[sp][dR](C).[sp][dR](C).[sp][dR](A).[sp][dR](G).[sp][dR](C).[sp][dR](G).[sp][dR](T).[sp][dR](G).[sp][dR](C).[sp][dR](G).[sp][dR](C).[sp][dR](C).[sp][dR](A).[sp][dR](T)}$$$$
IUPAC
P-thio-thymidylyl-(3'->5')-2'-deoxy-P-thio-cytidylyl-(3'->5')-P-thio-thymidylyl-(3'->5')-2'-deoxy-P-thio-cytidylyl-(3'->5')-2'-deoxy-P-thio-cytidylyl-(3'->5')-2'-deoxy-P-thio-cytidylyl-(3'->5')-2'-deoxy-P-thio-adenylyl-(3'->5')-2'-deoxy-P-thio-guanylyl-(3'->5')-2'-deoxy-P-thio-cytidylyl-(3'->5')-2'-deoxy-P-thio-guanylyl-(3'->5')-P-thio-thymidylyl-(3'->5')-2'-deoxy-P-thio-guanylyl-(3'->5')-2'-deoxy-P-thio-cytidylyl-(3'->5')-2'-deoxy-P-thio-guanylyl-(3'->5')-2'-deoxy-P-thio-cytidylyl-(3'->5')-2'-deoxy-P-thio-cytidylyl-(3'->5')-2'-deoxy-P-thio-adenylyl-(3'->5')-thymidine

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

1-[(2R,4S,5R)-5-[[[(2R,3S,5R)-2-[[[(2R,3S,5R)-2-[[[(2R,3S,5R)-2-[[[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-2-[[[(2R,3S,5R)-2-[[[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-2-[[[(2R,3S,5R)-2-[[[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-2-[[[(2R,3S,5R)-2-[[[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-2-[[[(2R,3S,5R)-2-[[[(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-2-[[[(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-2-[[[(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-2-[[[(2R,3S,5R)-2-[[[(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-2-[[hydroxy-[(2R,3S,5R)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(6-aminopurin-9-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(6-aminopurin-9-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C172H221N62O91P17S17/c1-69-39-225(169(253)213-149(69)237)117-21-73(236)92(292-117)44-274-326(257,343)320-85-33-129(229-63-191-135-141(181)187-61-189-143(135)229)303-103(85)55-285-332(263,349)314-79-27-122(221-17-9-113(177)201-165(221)249)295-95(79)47-278-330(261,347)312-78-26-121(220-16-8-112(176)200-164(220)248)298-98(78)50-280-338(269,355)322-87-35-131(231-65-193-137-145(231)205-157(183)209-153(137)241)305-105(87)57-287-334(265,351)316-81-29-124(223-19-11-115(179)203-167(223)251)299-99(81)51-281-339(270,356)323-88-36-132(232-66-194-138-146(232)206-158(184)210-154(138)242)307-107(88)59-289-337(268,354)319-84-32-128(228-42-72(4)152(240)216-172(228)256)302-102(84)54-284-341(272,358)325-90-38-134(234-68-196-140-148(234)208-160(186)212-156(140)244)306-106(90)58-288-335(266,352)317-82-30-125(224-20-12-116(180)204-168(224)252)300-100(82)52-282-340(271,357)324-89-37-133(233-67-195-139-147(233)207-159(185)211-155(139)243)308-108(89)60-290-342(273,359)321-86-34-130(230-64-192-136-142(182)188-62-190-144(136)230)304-104(86)56-286-333(264,350)315-80-28-123(222-18-10-114(178)202-166(222)250)296-96(80)48-277-328(259,345)310-76-24-119(218-14-6-110(174)198-162(218)246)294-94(76)46-276-329(260,346)311-77-25-120(219-15-7-111(175)199-163(219)247)297-97(77)49-279-336(267,353)318-83-31-127(227-41-71(3)151(239)215-171(227)255)301-101(83)53-283-331(262,348)313-75-23-118(217-13-5-109(173)197-161(217)245)293-93(75)45-275-327(258,344)309-74-22-126(291-91(74)43-235)226-40-70(2)150(238)214-170(226)254/h5-20,39-42,61-68,73-108,117-134,235-236H,21-38,43-60H2,1-4H3,(H,257,343)(H,258,344)(H,259,345)(H,260,346)(H,261,347)(H,262,348)(H,263,349)(H,264,350)(H,265,351)(H,266,352)(H,267,353)(H,268,354)(H,269,355)(H,270,356)(H,271,357)(H,272,358)(H,273,359)(H2,173,197,245)(H2,174,198,246)(H2,175,199,247)(H2,176,200,248)(H2,177,201,249)(H2,178,202,250)(H2,179,203,251)(H2,180,204,252)(H2,181,187,189)(H2,182,188,190)(H,213,237,253)(H,214,238,254)(H,215,239,255)(H,216,240,256)(H3,183,205,209,241)(H3,184,206,210,242)(H3,185,207,211,243)(H3,186,208,212,244)/t73-,74-,75-,76-,77-,78-,79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,89-,90-,91+,92+,93+,94+,95+,96+,97+,98+,99+,100+,101+,102+,103+,104+,105+,106+,107+,108+,117+,118+,119+,120+,121+,122+,123+,124+,125+,126+,127+,128+,129+,130+,131+,132+,133+,134+,326?,327?,328?,329?,330?,331?,332?,333?,334?,335?,336?,337?,338?,339?,340?,341?,342?/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

MIMNFCVQODTQDP-NDLVEFNKSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.4 SMILES

CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=S)(O)O[C@H]3C[C@@H](O[C@@H]3COP(=S)(O)O[C@H]4C[C@@H](O[C@@H]4COP(=S)(O)O[C@H]5C[C@@H](O[C@@H]5COP(=S)(O)O[C@H]6C[C@@H](O[C@@H]6COP(=S)(O)O[C@H]7C[C@@H](O[C@@H]7COP(=S)(O)O[C@H]8C[C@@H](O[C@@H]8COP(=S)(O)O[C@H]9C[C@@H](O[C@@H]9COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1COP(=S)(O)O[C@H]1C[C@@H](O[C@@H]1CO)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=CC(=NC1=O)N)N1C=CC(=NC1=O)N)N1C=NC2=C(N=CN=C21)N)N1C=NC2=C1N=C(NC2=O)N)N1C=CC(=NC1=O)N)N1C=NC2=C1N=C(NC2=O)N)N1C=C(C(=O)NC1=O)C)N1C=NC2=C1N=C(NC2=O)N)N1C=CC(=NC1=O)N)N1C=NC2=C1N=C(NC2=O)N)N1C=CC(=NC1=O)N)N1C=CC(=NC1=O)N)N1C=NC2=C(N=CN=C21)N)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C172H221N62O91P17S17
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

190977-41-4

3.3.2 DrugBank ID

3.3.3 NCI Thesaurus Code

3.3.4 Wikipedia

3.4 Synonyms

3.4.1 MeSH Entry Terms

  • bcl-2 antisense oligodeoxynucleotide
  • DNA, D(P-thio)(T-C-T-C-C-C-A-G-C-G-T-G-C-G-C-C-A-T)
  • DNA, D(P-thio)(T-C-T-C-C-C-A-G-C-G-T-G-C-G-C-C-A-T) hepatadecasodium salt
  • G 3139
  • G-3139 oligonucleotide
  • G3139
  • G3139 oligonucleotide
  • Genasense
  • oblimersen
  • oblimersen sodium

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
5685 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
-8.3
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
41
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
124
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
104
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
5681.5396694 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
5680.5363146 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
2560 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
359
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
16500
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
54
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
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 2021.10.14)

4.2 Chemical Classes

4.2.1 Drugs

4.2.1.1 Human Drugs
Human drugs -> EMA Drug Category

6 Drug and Medication Information

6.1 Clinical Trials

6.1.1 ClinicalTrials.gov

6.1.2 EU Clinical Trials Register

6.2 EMA Drug Information

Medicine
Category
Human drugs
Therapeutic area
Melanoma
Active Substance
oblimersen
INN/Common name
oblimersen
Status
Refused
Company
Genta Development Ltd. c/o Ross Craig

7 Pharmacology and Biochemistry

7.1 MeSH Pharmacological Classification

Antineoplastic Agents
Substances that inhibit or prevent the proliferation of NEOPLASMS. (See all compounds classified as Antineoplastic Agents.)
Oligodeoxyribonucleotides, Antisense
Short fragments of DNA that are used to alter the function of target RNAs or DNAs to which they hybridize. (See all compounds classified as Oligodeoxyribonucleotides, Antisense.)

7.2 ATC Code

L - Antineoplastic and immunomodulating agents

L01 - Antineoplastic agents

L01X - Other antineoplastic agents

L01XX - Other antineoplastic agents

L01XX36 - Oblimersen

8 Use and Manufacturing

8.1 Uses

8.1.1 Use Classification

Human drugs -> EMA Drug Category

9 Literature

9.1 Consolidated References

9.2 NLM Curated PubMed Citations

9.3 Springer Nature References

9.4 Chemical Co-Occurrences in Literature

9.5 Chemical-Gene Co-Occurrences in Literature

9.6 Chemical-Disease Co-Occurrences in Literature

10 Patents

10.1 Depositor-Supplied Patent Identifiers

10.2 WIPO PATENTSCOPE

10.3 Chemical Co-Occurrences in Patents

10.4 Chemical-Disease Co-Occurrences in Patents

10.5 Chemical-Gene Co-Occurrences in Patents

11 Interactions and Pathways

11.1 Drug-Drug Interactions

12 Classification

12.1 MeSH Tree

12.2 WHO ATC Classification System

12.3 MolGenie Organic Chemistry Ontology

13 Information Sources

  1. ClinicalTrials.gov
    LICENSE
    The ClinicalTrials.gov data carry an international copyright outside the United States and its Territories or Possessions. Some ClinicalTrials.gov data may be subject to the copyright of third parties; you should consult these entities for any additional terms of use.
    https://clinicaltrials.gov/ct2/about-site/terms-conditions#Use
  2. DrugBank
    LICENSE
    Creative Common's Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/legalcode)
    https://www.drugbank.ca/legal/terms_of_use
  3. EU Clinical Trials Register
  4. European Medicines Agency (EMA)
    LICENSE
    Information on the European Medicines Agency's (EMA) website is subject to a disclaimer and copyright and limited reproduction notices.
    https://www.ema.europa.eu/en/about-us/legal-notice
  5. NCI Thesaurus (NCIt)
    LICENSE
    Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source.
    https://www.cancer.gov/policies/copyright-reuse
  6. Springer Nature
  7. WHO Anatomical Therapeutic Chemical (ATC) Classification
    LICENSE
    Use of all or parts of the material requires reference to the WHO Collaborating Centre for Drug Statistics Methodology. Copying and distribution for commercial purposes is not allowed. Changing or manipulating the material is not allowed.
    https://www.whocc.no/copyright_disclaimer/
  8. Wikipedia
  9. PubChem
  10. 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
    Oligodeoxyribonucleotides, Antisense
    https://www.ncbi.nlm.nih.gov/mesh/68020319
  11. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  12. PATENTSCOPE (WIPO)
CONTENTS