oblimersen   Click here for help

GtoPdb Ligand ID: 8269

Synonyms: DNA, D(P-thio)(T-C-T-C-C-C-A-G-C-G-T-G-C-G-C-C-A-T) | G3139 | Genasense®
Compound class: Synthetic organic
Comment: Oblimersen is an 18mer phosphorothioate DNA antisense oligonucleotide complementary to the first six codons of the open reading frame of Bcl-2 messenger RNA. The sequence is 5′-tct ccc agc gtg cgc cat-3′ [1].
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 153
Hydrogen bond donors 41
Rotatable bonds 104
Topological polar surface area 2708.79
Molecular weight 5684.64
XLogP -6.43
No. Lipinski's rules broken 4
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES CC1=CN([C@H]2C[C@@H]([C@@H](COP(=S)(O)O[C@H]3C[C@H](N4C=NC5=C4N=CN=C5N)O[C@@H]3COP(=S)(O)O[C@H]6C[C@H](N7C=CC(=NC7=O)N)O[C@@H]6COP(=S)(O)O[C@H]8C[C@H](N9C=CC(=NC9=O)N)O[C@@H]8COP(=S)(O)O[C@H]%10C[C@H](N%11C=NC%12=C%11N=C(N)NC%12=O)O[C@@H]%10COP(=S)(O)O[C@H]%13C[C@H](N%14C=CC(=NC%14=O)N)O[C@@H]%13COP(=S)(O)O[C@H]%15C[C@H](N%16C=NC%17=C%16N=C(N)NC%17=O)O[C@@H]%15COP(=S)(O)O[C@H]%18C[C@H](N%19C=C(C)C(=O)NC%19=O)O[C@@H]%18COP(=S)(O)O[C@H]%20C[C@H](N%21C=NC%22=C%21N=C(N)NC%22=O)O[C@@H]%20COP(=S)(O)O[C@H]%23C[C@H](N%24C=CC(=NC%24=O)N)O[C@@H]%23COP(=S)(O)O[C@H]%25C[C@H](N%26C=NC%27=C%26N=C(N)NC%27=O)O[C@@H]%25COP(=S)(O)O[C@H]%28C[C@H](N%29C=NC%30=C%29N=CN=C%30N)O[C@@H]%28COP(=S)(O)O[C@H]%31C[C@H](N%32C=CC(=NC%32=O)N)O[C@@H]%31COP(=S)(O)O[C@H]%33C[C@H](N%34C=CC(=NC%34=O)N)O[C@@H]%33COP(=S)(O)O[C@H]%35C[C@H](N%36C=CC(=NC%36=O)N)O[C@@H]%35COP(=S)(O)O[C@H]%37C[C@H](N%38C=C(C)C(=O)NC%38=O)O[C@@H]%37COP(=S)(O)O[C@H]%39C[C@H](N%40C=CC(=NC%40=O)N)O[C@@H]%39COP(=S)(O)O[C@H]%41C[C@H](N%42C=C(C)C(=O)NC%42=O)O[C@@H]%41CO)O2)O)C(=O)NC1=O
Isomeric 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]%10C[C@@H](O[C@@H]%10COP(=S)(O)O[C@H]%11C[C@@H](O[C@@H]%11COP(=S)(O)O[C@H]%12C[C@@H](O[C@@H]%12COP(=S)(O)O[C@H]%13C[C@@H](O[C@@H]%13COP(=S)(O)O[C@H]%14C[C@@H](O[C@@H]%14COP(=S)(O)O[C@H]%15C[C@@H](O[C@@H]%15COP(=S)(O)O[C@H]%16C[C@@H](O[C@@H]%16COP(=S)(O)O[C@H]%17C[C@@H](O[C@@H]%17COP(=S)(O)O[C@H]%18C[C@@H](O[C@@H]%18COP(=S)(O)O[C@H]%19C[C@@H](O[C@@H]%19CO)N%20C=C(C(=O)NC%20=O)C)N%21C=CC(=NC%21=O)N)N%22C=C(C(=O)NC%22=O)C)N%23C=CC(=NC%23=O)N)N%24C=CC(=NC%24=O)N)N%25C=CC(=NC%25=O)N)N%26C=NC%27=C(N=CN=C%27%26)N)N%28C=NC%29=C%28N=C(NC%29=O)N)N%30C=CC(=NC%30=O)N)N%31C=NC%32=C%31N=C(NC%32=O)N)N%33C=C(C(=O)NC%33=O)C)N%34C=NC%35=C%34N=C(NC%35=O)N)N%36C=CC(=NC%36=O)N)N%37C=NC%38=C%37N=C(NC%38=O)N)N%39C=CC(=NC%39=O)N)N%40C=CC(=NC%40=O)N)N%41C=NC%42=C(N=CN=C%42%41)N)O
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
InChI Key MIMNFCVQODTQDP-NDLVEFNKSA-N
No information available.
Summary of Clinical Use Click here for help
The FDA has granted oblimersen orphan drug designation for the treatment of multiple myeloma (MM), acute myelocytic leukemia (AML), chronic lymphocytic leukemia (CLL) and advanced malignant melanoma. The efficacy of oblimersen has been assessed in many Phase 3 clinical trials, for several types of solid malignancies and lymphomas. It should be noted that several of these studies were terminated early. Click here to link to ClinicalTrials.gov's list of Phase 3 oblimersen trials.
Mechanism Of Action and Pharmacodynamic Effects Click here for help
Bcl-2 is an important apoptosis-regulating protein associated with chemoresistance and inhibition of apoptisis in malignant cells. Using an antisense technique to block the translation of Bcl-2 mRNA in to protein has an antitumour effect [1].