Target type: biologicalprocess
Repair of the damaged strand by the combined action of an apurinic endouclease that degrades a few bases on the damaged strand and a polymerase that synthesizes a 'patch' in the 5' to 3' direction, using the undamaged strand as a template. [ISBN:1550091131]
Base-excision repair (BER) is a major DNA repair pathway that removes damaged or modified bases from DNA. It involves a series of steps, including: 1) Recognition and removal of the damaged base by a DNA glycosylase. This enzyme cleaves the glycosidic bond between the damaged base and the deoxyribose sugar in the DNA backbone, creating an apurinic/apyrimidinic (AP) site. 2) The AP site is then processed by an AP endonuclease, which cleaves the phosphodiester bond 5' to the AP site, leaving a single-stranded gap. 3) The gap is then filled by DNA polymerase, which uses the undamaged strand as a template to synthesize a new DNA strand. 4) Finally, the newly synthesized DNA strand is sealed by DNA ligase, restoring the integrity of the DNA molecule. The gap-filling step in BER is crucial for repairing DNA damage and maintaining genomic stability. It involves the recruitment of DNA polymerase and the subsequent synthesis of a new DNA strand using the undamaged strand as a template. This process is highly accurate and efficient, ensuring that the damaged base is replaced with the correct nucleotide.'
"
| Protein | Definition | Taxonomy |
|---|---|---|
| Endonuclease 8-like 1 | An endonuclease 8-like 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96FI4] | Homo sapiens (human) |
| Poly(ADP-ribose) glycohydrolase | A poly(ADP-ribose) glycohydrolase that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q86W56] | Homo sapiens (human) |
| Flap endonuclease 1 | A flap endonuclease 1 that is encoded in the genome of human. [PRO:DNx] | Homo sapiens (human) |
| DNA-(apurinic or apyrimidinic site) endonuclease | A DNA-(apurinic or apyrimidinic site) endonuclease that is encoded in the genome of human. [PRO:DNx, UniProtKB:P27695] | Homo sapiens (human) |
| DNA ligase 1 | A DNA ligase 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P18858] | Homo sapiens (human) |
| DNA polymerase beta | A DNA polymerase beta that is encoded in the genome of human. [PRO:CNA] | Homo sapiens (human) |
| DNA polymerase lambda | A DNA polymerase lambda that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UGP5] | Homo sapiens (human) |
| Endonuclease 8-like 1 | An endonuclease 8-like 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96FI4] | Homo sapiens (human) |
| Poly(ADP-ribose) glycohydrolase | A poly(ADP-ribose) glycohydrolase that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q86W56] | Homo sapiens (human) |
| DNA polymerase subunit gamma-1 | A DNA polymerase subunit gamma-1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P54098] | Homo sapiens (human) |
| Flap endonuclease 1 | A flap endonuclease 1 that is encoded in the genome of human. [PRO:DNx] | Homo sapiens (human) |
| DNA polymerase delta catalytic subunit | A DNA polymerase delta catalytic subunit that is encoded in the genome of human. [PRO:DNx, UniProtKB:P28340] | Homo sapiens (human) |
| DNA-(apurinic or apyrimidinic site) endonuclease | A DNA-(apurinic or apyrimidinic site) endonuclease that is encoded in the genome of human. [PRO:DNx, UniProtKB:P27695] | Homo sapiens (human) |
| DNA ligase 1 | A DNA ligase 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P18858] | Homo sapiens (human) |
| Proliferating cell nuclear antigen | A proliferating cell nuclear antigen that is encoded in the genome of human. [PRO:DNx] | Homo sapiens (human) |
| DNA polymerase beta | A DNA polymerase beta that is encoded in the genome of human. [PRO:CNA] | Homo sapiens (human) |
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| digallic acid | digallic acid: structure given in first source | benzoate ester; gallate ester | |
| aurintricarboxylic acid | aurintricarboxylic acid : A member of the class of quinomethanes that is 3-methylidene-6-oxocyclohexa-1,4-diene-1-carboxylic acid in which the methylidene hydrogens are replaced by 4-carboxy-3-hydroxyphenyl groups. The trisodium salt is the biological stain 'chrome violet CG' while the triammonium salt is 'aluminon'. Aurintricarboxylic Acid: A dye which inhibits protein biosynthesis at the initial stages. The ammonium salt (aluminon) is a reagent for the colorimetric estimation of aluminum in water, foods, and tissues. | monohydroxybenzoic acid; quinomethanes; tricarboxylic acid | fluorochrome; histological dye; insulin-like growth factor receptor 1 antagonist |
| benzamide | benzamide : An aromatic amide that consists of benzene bearing a single carboxamido substituent. The parent of the class of benzamides. | benzamides | |
| chloroquine | chloroquine : An aminoquinoline that is quinoline which is substituted at position 4 by a [5-(diethylamino)pentan-2-yl]amino group at at position 7 by chlorine. It is used for the treatment of malaria, hepatic amoebiasis, lupus erythematosus, light-sensitive skin eruptions, and rheumatoid arthritis. Chloroquine: The prototypical antimalarial agent with a mechanism that is not well understood. It has also been used to treat rheumatoid arthritis, systemic lupus erythematosus, and in the systemic therapy of amebic liver abscesses. | aminoquinoline; organochlorine compound; secondary amino compound; tertiary amino compound | anticoronaviral agent; antimalarial; antirheumatic drug; autophagy inhibitor; dermatologic drug |
| foscarnet | Foscarnet: An antiviral agent used in the treatment of cytomegalovirus retinitis. Foscarnet also shows activity against human herpesviruses and HIV. phosphonoformic acid : Phosphoric acid in which one of the hydroxy groups is replaced by a carboxylic acid group. It is used as the trisodium salt as an antiviral agent in the treatment of cytomegalovirus retinitis (CMV retinitis, an inflamation of the retina that can lead to blindness) and as an alternative to ganciclovir for AIDS patients who require concurrent antiretroviral therapy but are unable to tolerate ganciclovir due to haematological toxicity. | carboxylic acid; one-carbon compound; phosphonic acids | antiviral drug; geroprotector; HIV-1 reverse transcriptase inhibitor; sodium-dependent Pi-transporter inhibitor |
| hycanthone | hycanthone : A thioxanthen-9-one compound having a hydroxymethyl substituent at the 1-position and a 2-[(diethylamino)ethyl]amino substituent at the 4-position. It was formerly used (particularly as the monomethanesulfonic acid salt) as a schistosomicide for individual or mass treatement of infection with Schistosoma haematobium and S. mansoni, but due to its toxicity and concern about possible carcinogenicity, it has been replaced by other drugs such as praziquantel. Hycanthone: Potentially toxic, but effective antischistosomal agent, it is a metabolite of LUCANTHONE. | thioxanthenes | mutagen; schistosomicide drug |
| isoniazid | Hydra: A genus of freshwater polyps in the family Hydridae, order Hydroida, class HYDROZOA. They are of special interest because of their complex organization and because their adult organization corresponds roughly to the gastrula of higher animals. hydrazide : Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC). | carbohydrazide | antitubercular agent; drug allergen |
| 3,3',5-triiodothyroacetic acid | tiratricol : A monocarboxylic acid that is (4-hydroxy-3,5-diiodophenyl)acetic acid in which the phenolic hydroxy group has been replaced by a 4-hydroxy-3-iodophenoxy group. It is a thyroid hormone analogue that has been used in the treatment of thyroid hormone resistance syndrome. | ||
| 3,3',5-triiodothyropropionic acid | aromatic ether | ||
| thyroxine | thyroxine : An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. Thyroxine: The major hormone derived from the thyroid gland. Thyroxine is synthesized via the iodination of tyrosines (MONOIODOTYROSINE) and the coupling of iodotyrosines (DIIODOTYROSINE) in the THYROGLOBULIN. Thyroxine is released from thyroglobulin by proteolysis and secreted into the blood. Thyroxine is peripherally deiodinated to form TRIIODOTHYRONINE which exerts a broad spectrum of stimulatory effects on cell metabolism. | 2-halophenol; iodophenol; L-phenylalanine derivative; non-proteinogenic L-alpha-amino acid; thyroxine; thyroxine zwitterion | antithyroid drug; human metabolite; mouse metabolite; thyroid hormone |
| triiodothyronine | 3,3',5-triiodo-L-thyronine : An iodothyronine compound having iodo substituents at the 3-, 3'- and 5-positions. Although some is produced in the thyroid, most of the 3,3',5-triiodo-L-thyronine in the body is generated by mono-deiodination of L-thyroxine in the peripheral tissues. Its metabolic activity is about 3 to 5 times that of L-thyroxine. The sodium salt is used in the treatment of hypothyroidism. Triiodothyronine: A T3 thyroid hormone normally synthesized and secreted by the thyroid gland in much smaller quantities than thyroxine (T4). Most T3 is derived from peripheral monodeiodination of T4 at the 5' position of the outer ring of the iodothyronine nucleus. The hormone finally delivered and used by the tissues is mainly T3. | 2-halophenol; amino acid zwitterion; iodophenol; iodothyronine | human metabolite; mouse metabolite; thyroid hormone |
| pamoic acid | pamoic acid: RN given refers to parent cpd; structure | dicarboxylic acid | |
| lucanthone | lucanthone : A thioxanthen-9-one compound having a methyl substituent at the 1-position and a 2-[(diethylamino)ethyl]amino substituent at the 4-position. Formerly used for the treatment of schistosomiasis. It is a prodrug, being metabolised to hycanthone. Lucanthone: One of the SCHISTOSOMICIDES, it has been replaced largely by HYCANTHONE and more recently PRAZIQUANTEL. (From Martindale The Extrapharmacopoeia, 30th ed., p46) | thioxanthenes | adjuvant; antineoplastic agent; EC 5.99.1.2 (DNA topoisomerase) inhibitor; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; mutagen; photosensitizing agent; prodrug; schistosomicide drug |
| Dillapiole | 5-allyl 6,7-dimethoxy 1,3-benzodioxole: a plant based insecticide; structure in first source | benzodioxoles | metabolite |
| oleanolic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | plant metabolite | |
| ochracin | ochracin: produced by Aspergillus alutaceus; structure in first source | isochromanes | |
| zidovudine | zidovudine : A pyrimidine 2',3'-dideoxyribonucleoside compound having a 3'-azido substituent and thymine as the nucleobase. Zidovudine: A dideoxynucleoside compound in which the 3'-hydroxy group on the sugar moiety has been replaced by an azido group. This modification prevents the formation of phosphodiester linkages which are needed for the completion of nucleic acid chains. The compound is a potent inhibitor of HIV replication, acting as a chain-terminator of viral DNA during reverse transcription. It improves immunologic function, partially reverses the HIV-induced neurological dysfunction, and improves certain other clinical abnormalities associated with AIDS. Its principal toxic effect is dose-dependent suppression of bone marrow, resulting in anemia and leukopenia. | azide; pyrimidine 2',3'-dideoxyribonucleoside | antimetabolite; antiviral drug; HIV-1 reverse transcriptase inhibitor |
| mitoxantrone hydrochloride | hydrochloride | antineoplastic agent | |
| ursolic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | geroprotector; plant metabolite | |
| thymidine 5'-triphosphate | dTTP : A thymidine phosphate having a triphosphate group at the 5'-position. thymidine 5'-triphosphate: RN given refers to parent cpd | pyrimidine 2'-deoxyribonucleoside 5'-triphosphate; thymidine phosphate | Escherichia coli metabolite; mouse metabolite |
| betulinic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | anti-HIV agent; anti-inflammatory agent; antimalarial; antineoplastic agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; plant metabolite | |
| calanolide a | (+)-calanolide A : An organic heterotetracyclic compound that is 11,12-dihydro-2H,6H,10H-dipyrano[2,3-f:2',3'-h]chromen-2-one substituted by a hydroxy group at position 12, methyl groups at positions 6, 6, 10 and 11 and a propyl group at position 4 (the 10R,11S,12S stereoisomer). Isolated from Calophyllum lanigerum var austrocoriaceum and Calophyllum brasiliense, it exhibits potent activity against HIV-1 reverse transcriptase. calanolide A: NSC 661122 and costatolide are isomers; a novel HIV-inhibitory class of coumarin derivatives from the tropical rainforest tree, Calophyllum lanigerum (Clusiaceae); structure in first source | cyclic ether; delta-lactone; organic heterotetracyclic compound; secondary alcohol | HIV-1 reverse transcriptase inhibitor; plant metabolite |
| 2',3'-dideoxythymidine triphosphate | ddTTP : A pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate having thymine as the nucleobase. | pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate; thymidine phosphate | |
| 2',3'-dideoxyadenosine triphosphate | purine deoxyribonucleoside triphosphate | ||
| zidovudine triphosphate | |||
| illimaquinone | illimaquinone: structure given in first source; isolated from the Red Sea sponge Smenospongia; inhibits the RNase H. activity of HIV-1 reverse transcriptase | monohydroxy-1,4-benzoquinones; prenylquinone | metabolite |
| 7-nitro-1h-indole-2-carboxylic acid | 7-nitro-1H-indole-2-carboxylic acid: acts on AP endonuclease, 3'-phosphodiesterase, and 3'-phosphatase activities of APE1; structure in first source | ||
| n-hydroxynaphthalimide | N-hydroxynaphthalimide: structure in first source | ||
| 3,5-diiodothyronine, (l)-isomer | phenylalanine derivative | ||
| 3,3',4,4',5,5'-hexabromobiphenyl | |||
| 3,3'-diiodothyronine | 3,3'-diiodothyronine: RN given refers to unlabeled cpd without isomeric designation | 3,3'-diiodothyronine; amino acid zwitterion | human metabolite |
| 6-hydroxydopa | 6-hydroxydopa: RN given refers to cpd without isomeric designation | non-proteinogenic alpha-amino acid | |
| 3,5-diiodothyropropionic acid | 3,5-diiodothyropropionic acid : A monocarboxylic acid that is (4-hydroxy-3,5-diiodophenyl)propanoic acid in which the phenolic hydroxy group has been replaced by a 4-hydroxyphenyl group. An ionotropic analogue of L-thyroxine. 3,5-diiodothyropropionic acid: a cardiotonic thyroid hormone analog | aromatic ether; monocarboxylic acid; organoiodine compound; phenols | |
| tanshinone ii a | tashinone IIA: a cardiovascular agent with antineoplastic activity; isolated from Salvia miltiorrhiza; structure in first source | abietane diterpenoid | |
| 3-hydroxy-quinazoline-2,4-dione | 3-hydroxy-quinazoline-2,4-dione: structure in first source | ||
| sitosterol, (3beta)-isomer | sitosterol : A member of the class of phytosterols that is stigmast-5-ene substituted by a beta-hydroxy group at position 3. Sobatum: tradename; active fraction of Solanum trilobatum; reduces side-effects of radiation-induced toxicity | 3beta-hydroxy-Delta(5)-steroid; 3beta-sterol; C29-steroid; phytosterols; stigmastane sterol | anticholesteremic drug; antioxidant; mouse metabolite; plant metabolite; sterol methyltransferase inhibitor |
| TTP | pyrimidine ribonucleoside 5'-triphosphate | ||
| aphidicolin | aphidicolin : A tetracyclic diterpenoid that has an tetradecahydro-8,11a-methanocyclohepta[a]naphthalene skeleton with two hydroxymethyl substituents at positions 4 and 9, two methyl substituents at positions 4 and 11b and two hydroxy substituents at positions 3 and 9. An antibiotic with antiviral and antimitotical properties. Aphidicolin is a reversible inhibitor of eukaryotic nuclear DNA replication. Aphidicolin: An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells. | tetracyclic diterpenoid | antimicrobial agent; antimitotic; antineoplastic agent; antiviral drug; apoptosis inducer; Aspergillus metabolite; DNA synthesis inhibitor; EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor; fungal metabolite |
| 1,3,6-trimethylpyrimido[5,4-e][1,2,4]triazine-5,7-dione | pyrimidotriazine | ||
| pnu183792 | PNU183792: structure in first source | ||
| 4-phenyl-4-oxo-2-hydroxybuten-2-oic acid | 2,4-dioxo-4-phenylbutanoic acid: structure in first source | ||
| 2-[[5-(dimethylsulfamoyl)-1H-indol-3-yl]methylidene]propanedioic acid diethyl ester | indoles | ||
| 1,6-dimethyl-3-propylpyrimido[5,4-e][1,2,4]triazine-5,7-dione | pyrimidotriazine | ||
| stigmasterol | stigmasta-5,22-dien-3-ol: isolated from freeze-dried powder of Blackberries (Rubus ursinus L.) which showed an activity on inhibition of chemocarcinogen stigmasterol : A 3beta-sterol that consists of 3beta-hydroxystigmastane having double bonds at the 5,6- and 22,23-positions. | 3beta-hydroxy-Delta(5)-steroid; 3beta-sterol; phytosterols; stigmastane sterol | plant metabolite |
| myricetin | 7-hydroxyflavonol; hexahydroxyflavone | antineoplastic agent; antioxidant; cyclooxygenase 1 inhibitor; food component; geroprotector; hypoglycemic agent; plant metabolite | |
| pecilocin | pecilocin: fungicidal antibiotic produced by Paecilomyces varioti Bainier var. antibioticus; structure | N-acylpyrrolidine | |
| ag 538 | AG 538: an IGF-1 receptor kinase inhibitor; structure in first source | ||
| lyoniside | daucosterol : A steroid saponin that is sitosterol attached to a beta-D-glucopyranosyl residue at position 3 via a glycosidic linkage. It has bee isolated from Panax japonicus var. major and Breynia fruticosa. | beta-D-glucoside; monosaccharide derivative; steroid saponin | plant metabolite |
| e 3330 | E 3330: structure given in first source; MW 378.47 | ||
| adenosine diphosphate (hydroxymethyl)pyrrolidinediol | dihydroxypyrrolidine; purine ribonucleoside 5'-diphosphate | ||
| corosolic acid | triterpenoid | metabolite | |
| oblongifolin c | oblongifolin C: has antineoplastic activity; isolated from Garcinia yunnanensis; structure in first source | ||
| ol-135 | |||
| edgeworin | edgeworin: from Dirca occidentalis Gray; structure given in first source | ||
| sch 725680 | Sch 725680: an aazaphilone from Aspergillus sp.; structure in first source | ||
| guttiferone k | guttiferone K: antiproliferative compound of Rheedia calcicola from the Madagascar rain forest; structure in first source | ||
| N-[3-(1,3-benzothiazol-2-yl)-5,6-dihydro-4H-thieno[2,3-c]pyrrol-2-yl]acetamide | benzothiazoles | ||
| raltegravir | 1,2,4-oxadiazole; dicarboxylic acid amide; hydroxypyrimidine; monofluorobenzenes; pyrimidone; secondary carboxamide | antiviral drug; HIV-1 integrase inhibitor | |
| GS-443902 | GS-441524 triphosphate: intracellular active metabolite of remdesivir GS-443902 : An organic triphosphate that is GS-441524 in which the 5'-hydroxy group has been replaced by a triphosphate group. It is the active metabolite of remdesivir. | aromatic amine; C-nucleoside; nitrile; organic triphosphate; pyrrolotriazine | anticoronaviral agent; antiviral drug; drug metabolite |
| pinophilin b | pinophilin B: from cultures of a fungus (Penicillium pinophilum Hedgcok) derived from a seaweed; structure in first source | ||
| deoxyguanosine triphosphate | deoxyguanosine phosphate; guanyl deoxyribonucleotide; purine 2'-deoxyribonucleoside 5'-triphosphate | Arabidopsis thaliana metabolite; Escherichia coli metabolite; human metabolite; mouse metabolite; plant metabolite; Saccharomyces cerevisiae metabolite | |
| thiolactomycin | thiolactomycin: from actinomycetes; structure given in first source | ||
| acyclovir triphosphate | |||
| galloflavin | galloflavin: structure in first source |