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CHEBI ONTOLOGY - ANNOTATIONS

The Chemical Entities of Biological Interest (ChEBI) ontology is downloaded weekly from EMBL-EBI at http://www.ebi.ac.uk/chebi/. The data is made available under the Creative Commons License (CC BY 3.0, http://creativecommons.org/licenses/by/3.0/). For more information see: Degtyarenko et al. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.

Term:romidepsin
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Accession:CHEBI:61080 term browser browse the term
Definition:A cyclodepsipeptide consisting of the cyclic disulfide of (2Z)-2-aminobut-2-enoyl, L-valyl, (3S,4E)-3-hydroxy-7-sulfanylhept-4-enoyl, D-valyl and D-cysteinyl residues coupled in sequence and cyclised head-to tail.
Synonyms:exact_synonym: (1S,4S,7Z,10S,16E,21R)-7-ethylidene-4,21-di(propan-2-yl)-2-oxa-12,13-dithia-5,8,20,23-tetraazabicyclo[8.7.6]tricos-16-ene-3,6,9,19,22-pentone
 related_synonym: Antibiotic FR 901228;   Chromadax;   FK228;   FR901228;   Formula=C24H36N4O6S2;   InChI=1S/C24H36N4O6S2/c1-6-16-21(30)28-20(14(4)5)24(33)34-15-9-7-8-10-35-36-12-17(22(31)25-16)26-23(32)19(13(2)3)27-18(29)11-15/h6-7,9,13-15,17,19-20H,8,10-12H2,1-5H3,(H,25,31)(H,26,32)(H,27,29)(H,28,30)/b9-7+,16-6-/t15-,17-,19-,20+/m1/s1;   InChIKey=OHRURASPPZQGQM-GCCNXGTGSA-N;   Istodax;   NSC-630176;   SMILES=C\\C=C1/NC(=O)[C@H]2CSSCC\\C=C\\[C@H](CC(=O)N[C@H](C(C)C)C(=O)N2)OC(=O)[C@@H](NC1=O)C(C)C;   romidepsina;   romidepsine;   romidepsinum
 alt_id: CHEBI:69482
 xref: CAS:128517-07-7;   Drug_Central:4119;   KEGG:D06637
 xref_mesh: MESH:C087123
 xref: PMID:18205373;   PMID:20645688;   PMID:21110829;   PMID:7513682;   PMID:8175483;   Reaxys:6854221;   Wikipedia:Romidepsin


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romidepsin term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb1a ATP binding cassette subfamily B member 1A decreases response to substance
multiple interactions
increases expression
increases acetylation
ISO ABCB1 protein results in decreased susceptibility to romidepsin
[[Tretinoin co-treated with romidepsin] results in increased expression of ABCB1 mRNA] which results in decreased susceptibility to Doxorubicin; [Tretinoin co-treated with romidepsin] results in increased expression of ABCB1 protein; ABCB1 protein binds to and affects the export of romidepsin; romidepsin promotes the reaction [Tretinoin results in increased expression of ABCB1 mRNA]; Tretinoin promotes the reaction [romidepsin results in increased acetylation of ABCB1 promoter]; valspodar inhibits the reaction [[[Tretinoin co-treated with romidepsin] results in increased expression of ABCB1 mRNA] which results in decreased susceptibility to Doxorubicin]
romidepsin results in increased expression of ABCB1 mRNA; romidepsin results in increased expression of ABCB1 protein
CTD PMID:15634944, PMID:15833893, PMID:16049968, PMID:16223781 NCBI chr 4:22,339,829...22,517,642
Ensembl chr 4:22,133,521...22,425,515
JBrowse link
G Abcc1 ATP binding cassette subfamily C member 1 multiple interactions
decreases response to substance
ISO ABCC1 protein binds to and affects the export of romidepsin
ABCC1 protein results in decreased susceptibility to romidepsin
CTD PMID:15634944, PMID:16049968 NCBI chr10:549,537...672,235
Ensembl chr10:549,883...672,196
JBrowse link
G Akt1 AKT serine/threonine kinase 1 multiple interactions
increases phosphorylation
ISO romidepsin inhibits the reaction [[PD 0325901 co-treated with MK 2206] results in increased phosphorylation of AKT1 protein]
romidepsin results in increased phosphorylation of AKT1 protein
CTD PMID:27634878 NCBI chr 6:137,218,398...137,239,970
Ensembl chr 6:137,218,376...137,236,258
JBrowse link
G Bak1 BCL2-antagonist/killer 1 multiple interactions
increases expression
ISO [romidepsin co-treated with MK 2206] results in increased expression of BAK1 protein; [romidepsin co-treated with PD 0325901 co-treated with MK 2206] results in increased expression of BAK1 protein; [romidepsin co-treated with PD 0325901] results in increased expression of BAK1 protein
romidepsin results in increased expression of BAK1 protein
CTD PMID:27634878 NCBI chr20:5,609,620...5,618,899
Ensembl chr20:5,609,625...5,618,260
JBrowse link
G Bcl2a1 BCL2-related protein A1 multiple interactions ISO [romidepsin co-treated with Bortezomib] results in decreased expression of BCL2A1 protein CTD PMID:18223231 NCBI chr 8:96,551,424...96,559,527
Ensembl chr 8:96,551,245...96,559,483
JBrowse link
G Bcl2l1 Bcl2-like 1 multiple interactions ISO [romidepsin co-treated with Bortezomib] results in decreased expression of BCL2L1 protein CTD PMID:18223231 NCBI chr 3:148,259,594...148,314,191
Ensembl chr 3:148,259,596...148,313,810
JBrowse link
G Bcl2l11 BCL2 like 11 multiple interactions
increases expression
ISO [Bortezomib co-treated with romidepsin] results in increased expression of BCL2L11 protein; [romidepsin co-treated with MK 2206] results in increased expression of BCL2L11 protein; [romidepsin co-treated with PD 0325901 co-treated with MK 2206] results in increased expression of BCL2L11 protein; [romidepsin co-treated with PD 0325901] results in increased expression of BCL2L11 protein; Acetylcysteine inhibits the reaction [[Bortezomib co-treated with romidepsin] results in increased expression of BCL2L11 protein]
romidepsin results in increased expression of BCL2L11 protein
CTD PMID:15069698, PMID:15173094, PMID:18223231, PMID:27634878 NCBI chr 3:120,726,906...120,764,192
Ensembl chr 3:120,726,906...120,764,192
JBrowse link
G Bdnf brain-derived neurotrophic factor multiple interactions EXP romidepsin inhibits the reaction [Dexamethasone results in decreased acetylation of BDNF exon]; romidepsin inhibits the reaction [Dexamethasone results in decreased expression of BDNF mRNA] CTD PMID:31518422 NCBI chr 3:100,768,637...100,819,216
Ensembl chr 3:100,768,637...100,819,210
JBrowse link
G Birc2 baculoviral IAP repeat-containing 2 multiple interactions ISO [romidepsin co-treated with Bortezomib] results in decreased expression of BIRC2 protein CTD PMID:18223231 NCBI chr 8:6,014,014...6,036,668
Ensembl chr 8:6,013,207...6,034,142
JBrowse link
G Birc5 baculoviral IAP repeat-containing 5 multiple interactions ISO [romidepsin co-treated with Bortezomib] results in increased cleavage of BIRC5 protein CTD PMID:18223231 NCBI chr10:106,856,097...106,864,419
Ensembl chr10:106,856,097...106,864,413
JBrowse link
G Casp3 caspase 3 increases activity
multiple interactions
increases cleavage
ISO romidepsin results in increased activity of CASP3 protein
alvocidib promotes the reaction [romidepsin results in increased activity of CASP3 protein]; Bortezomib promotes the reaction [romidepsin results in increased cleavage of CASP3 protein]
CTD PMID:15014036, PMID:18223231 NCBI chr16:48,845,011...48,863,249
Ensembl chr16:48,845,012...48,863,204
JBrowse link
G Casp9 caspase 9 multiple interactions
increases cleavage
ISO Bortezomib promotes the reaction [romidepsin results in increased cleavage of CASP9 protein] CTD PMID:18223231 NCBI chr 5:160,356,211...160,373,774
Ensembl chr 5:160,355,833...160,373,778
JBrowse link
G Ccna2 cyclin A2 decreases expression ISO romidepsin results in decreased expression of CCNA2 protein CTD PMID:15014036 NCBI chr 2:123,274,727...123,282,266
Ensembl chr 2:123,275,881...123,282,214
JBrowse link
G Ccnb1 cyclin B1 decreases expression ISO romidepsin results in decreased expression of CCNB1 protein CTD PMID:15014036 NCBI chr 2:30,782,133...30,791,106
Ensembl chr 2:30,783,915...30,791,221
JBrowse link
G Cdkn1a cyclin-dependent kinase inhibitor 1A multiple interactions
increases expression
ISO alvocidib inhibits the reaction [romidepsin results in increased expression of CDKN1A promoter]; alvocidib inhibits the reaction [romidepsin results in increased expression of CDKN1A protein]; Aspirin promotes the reaction [romidepsin results in increased expression of CDKN1A protein]; calphostin C inhibits the reaction [romidepsin results in increased expression of CDKN1A protein]; Dichlororibofuranosylbenzimidazole inhibits the reaction [romidepsin results in increased expression of CDKN1A protein]; Phorbol 12,13-Dibutyrate inhibits the reaction [alvocidib inhibits the reaction [romidepsin results in increased expression of CDKN1A protein]]; PTGS1 mutant form inhibits the reaction [Aspirin promotes the reaction [romidepsin results in increased expression of CDKN1A protein]]; romidepsin promotes the reaction [Tretinoin results in increased expression of CDKN1A mRNA]
romidepsin results in increased expression of CDKN1A mRNA; romidepsin results in increased expression of CDKN1A promoter; romidepsin results in increased expression of CDKN1A protein
CTD PMID:15014036, PMID:15849726, PMID:16223781, PMID:17230511, PMID:20404564 NCBI chr20:6,348,422...6,358,864
Ensembl chr20:6,351,458...6,358,864
JBrowse link
G Cflar CASP8 and FADD-like apoptosis regulator multiple interactions ISO [romidepsin co-treated with Bortezomib] results in decreased expression of CFLAR protein CTD PMID:18223231 NCBI chr 9:65,534,608...65,586,395
Ensembl chr 9:65,534,704...65,587,251
JBrowse link
G Cyp1a1 cytochrome P450, family 1, subfamily a, polypeptide 1 affects metabolic processing ISO CYP1A1 protein affects the metabolism of romidepsin CTD PMID:15635176 NCBI chr 8:62,472,087...62,478,122
Ensembl chr 8:62,472,095...62,478,147
JBrowse link
G Cyp2b3 cytochrome P450, family 2, subfamily b, polypeptide 3 affects metabolic processing ISO CYP2B6 protein affects the metabolism of romidepsin CTD PMID:15635176 NCBI chr 1:83,163,103...83,236,615
Ensembl chr 1:83,163,079...83,236,615
JBrowse link
G Cyp3a9 cytochrome P450, family 3, subfamily a, polypeptide 9 affects metabolic processing ISO CYP3A5 protein affects the metabolism of romidepsin CTD PMID:15635176 NCBI chr12:19,074,288...19,114,491
Ensembl chr12:19,074,583...19,114,399
JBrowse link
G Egfr epidermal growth factor receptor decreases expression ISO romidepsin results in decreased expression of EGFR protein CTD PMID:15014036 NCBI chr14:99,919,485...100,104,136
Ensembl chr14:99,919,485...100,098,796
JBrowse link
G Erbb2 erb-b2 receptor tyrosine kinase 2 decreases expression ISO romidepsin results in decreased expression of ERBB2 protein CTD PMID:15014036 NCBI chr10:86,367,596...86,391,728
Ensembl chr10:86,367,596...86,391,728
JBrowse link
G Ewsr1 EWS RNA-binding protein 1 multiple interactions
decreases expression
ISO romidepsin results in decreased activity of and results in decreased expression of EWSR1 protein mutant form
romidepsin results in decreased expression of EWSR1 mRNA mutant form
CTD PMID:15849726 NCBI chr14:85,322,105...85,350,826
Ensembl chr14:85,322,296...85,350,948
JBrowse link
G Fli1 Fli-1 proto-oncogene, ETS transcription factor multiple interactions
decreases expression
ISO romidepsin results in decreased activity of and results in decreased expression of FLI1 protein mutant form
romidepsin results in decreased expression of FLI1 mRNA mutant form
CTD PMID:15849726 NCBI chr 8:33,541,932...33,661,111
Ensembl chr 8:33,543,258...33,661,049
JBrowse link
G Folr2 folate receptor beta multiple interactions ISO romidepsin promotes the reaction [Tretinoin results in increased expression of FOLR2 mRNA]; romidepsin promotes the reaction [Tretinoin results in increased expression of FOLR2 protein] CTD PMID:16740727 NCBI chr 1:166,915,045...166,933,377
Ensembl chr 1:166,915,045...166,919,302
JBrowse link
G H2ax H2A.X variant histone multiple interactions ISO [Bortezomib co-treated with romidepsin] results in increased phosphorylation of H2AX protein; Acetylcysteine inhibits the reaction [[Bortezomib co-treated with romidepsin] results in increased phosphorylation of H2AX protein] CTD PMID:15173094 NCBI chr 8:48,665,652...48,666,981
Ensembl chr 8:48,665,652...48,666,981
JBrowse link
G H3f4 H3.4 histone increases acetylation ISO romidepsin results in increased acetylation of H3-4 protein CTD PMID:16006969 NCBI chr10:45,304,696...45,305,106 JBrowse link
G Hdac2 histone deacetylase 2 multiple interactions EXP romidepsin inhibits the reaction [Dexamethasone results in decreased expression of HDAC2 protein] CTD PMID:31518422 NCBI chr20:43,084,870...43,108,198
Ensembl chr20:43,084,870...43,108,198
JBrowse link
G Hif1a hypoxia inducible factor 1 subunit alpha multiple interactions ISO romidepsin inhibits the reaction [cobaltous chloride results in increased expression of HIF1A protein] CTD PMID:21295294 NCBI chr 6:96,810,868...96,856,303
Ensembl chr 6:96,810,907...96,856,052
JBrowse link
G Icam1 intercellular adhesion molecule 1 multiple interactions ISO [romidepsin co-treated with Bortezomib] results in decreased expression of ICAM1 protein CTD PMID:18223231 NCBI chr 8:22,035,287...22,047,049
Ensembl chr 8:22,035,256...22,047,059
JBrowse link
G Mapk1 mitogen activated protein kinase 1 multiple interactions ISO romidepsin results in decreased activity of and results in decreased phosphorylation of MAPK1 protein CTD PMID:15014036 NCBI chr11:88,203,863...88,273,301
Ensembl chr11:88,211,599...88,273,254
JBrowse link
G Mapk3 mitogen activated protein kinase 3 multiple interactions ISO romidepsin results in decreased activity of and results in decreased phosphorylation of MAPK3 protein CTD PMID:15014036 NCBI chr 1:198,192,773...198,198,975
Ensembl chr 1:198,192,773...198,198,975
JBrowse link
G Mcl1 MCL1 apoptosis regulator, BCL2 family member multiple interactions
increases expression
ISO [romidepsin co-treated with MK 2206] results in increased expression of MCL1 protein; [romidepsin co-treated with PD 0325901 co-treated with MK 2206] results in increased expression of MCL1 protein; [romidepsin co-treated with PD 0325901] results in increased expression of MCL1 protein; romidepsin inhibits the reaction [Bortezomib results in increased expression of MCL1 protein]
romidepsin results in increased expression of MCL1 protein
CTD PMID:18223231, PMID:27634878 NCBI chr 2:197,786,212...197,788,992 JBrowse link
G Nfkb1 nuclear factor kappa B subunit 1 multiple interactions
increases expression
ISO Bortezomib inhibits the reaction [romidepsin results in increased expression of NFKB1 protein] CTD PMID:18223231 NCBI chr 2:240,773,520...240,890,053
Ensembl chr 2:240,773,456...240,866,689
JBrowse link
G Nfkbia NFKB inhibitor alpha increases expression
multiple interactions
ISO romidepsin results in increased expression of NFKBIA protein
Bortezomib inhibits the reaction [romidepsin results in increased expression of NFKBIA protein]
CTD PMID:18223231 NCBI chr 6:76,267,227...76,270,457
Ensembl chr 6:76,267,228...76,270,457
JBrowse link
G Nr1i3 nuclear receptor subfamily 1, group I, member 3 increases expression ISO romidepsin results in increased expression of NR1I3 mRNA CTD PMID:16006969 NCBI chr13:89,585,072...89,591,278
Ensembl chr13:89,586,283...89,591,277
JBrowse link
G Parp1 poly (ADP-ribose) polymerase 1 multiple interactions
increases cleavage
ISO [romidepsin co-treated with MK 2206] results in increased cleavage of PARP1 protein; Bortezomib promotes the reaction [romidepsin results in increased cleavage of PARP1 protein]; romidepsin promotes the reaction [[PD 0325901 co-treated with MK 2206] results in increased cleavage of PARP1 protein]; romidepsin promotes the reaction [PD 0325901 results in increased cleavage of PARP1 protein] CTD PMID:18223231, PMID:27634878 NCBI chr13:98,857,255...98,889,444
Ensembl chr13:98,857,177...98,889,716
JBrowse link
G Ptgs1 prostaglandin-endoperoxide synthase 1 multiple interactions ISO PTGS1 mutant form inhibits the reaction [Aspirin promotes the reaction [romidepsin results in increased expression of CDKN1A protein]] CTD PMID:20404564 NCBI chr 3:15,560,685...15,582,339
Ensembl chr 3:15,560,712...15,582,344
JBrowse link
G Raf1 Raf-1 proto-oncogene, serine/threonine kinase decreases expression ISO romidepsin results in decreased expression of RAF1 protein CTD PMID:15014036 NCBI chr 4:147,532,040...147,592,769
Ensembl chr 4:147,532,042...147,592,699
JBrowse link
G Rb1 RB transcriptional corepressor 1 decreases phosphorylation ISO romidepsin results in decreased phosphorylation of RB1 protein CTD PMID:15014036, PMID:15849726 NCBI chr15:55,081,582...55,209,060
Ensembl chr15:55,083,140...55,209,342
JBrowse link
G Rela RELA proto-oncogene, NF-kB subunit multiple interactions
decreases response to substance
increases acetylation
ISO Bortezomib inhibits the reaction [romidepsin results in increased acetylation of RELA protein]
RELA protein results in decreased susceptibility to romidepsin
CTD PMID:18223231 NCBI chr 1:220,992,770...221,003,249
Ensembl chr 1:220,992,770...221,003,249
JBrowse link
G Slc1a2 solute carrier family 1 member 2 multiple interactions
increases expression
EXP romidepsin inhibits the reaction [Manganese results in decreased expression of SLC1A2 mRNA]
romidepsin results in increased expression of SLC1A2 mRNA
CTD PMID:24469401 NCBI chr 3:92,518,679...92,665,731
Ensembl chr 3:92,640,752...92,665,644
JBrowse link
G Vegfa vascular endothelial growth factor A decreases expression
multiple interactions
ISO romidepsin results in decreased expression of VEGFA mRNA
romidepsin results in decreased expression of and results in decreased secretion of VEGFA protein
CTD PMID:21295294 NCBI chr 9:17,340,341...17,355,681
Ensembl chr 9:17,340,341...17,355,681
JBrowse link
G Xiap X-linked inhibitor of apoptosis multiple interactions ISO [romidepsin co-treated with Bortezomib] results in decreased expression of XIAP protein CTD PMID:18223231 NCBI chr  X:128,409,425...128,455,786
Ensembl chr  X:128,409,472...128,453,000
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  CHEBI ontology 19785
    role 19732
      biological role 19732
        antimicrobial agent 17309
          heterocyclic antibiotic 1611
            romidepsin 43
Path 2
Term Annotations click to browse term
  CHEBI ontology 19785
    subatomic particle 19782
      composite particle 19782
        hadron 19782
          baryon 19782
            nucleon 19782
              atomic nucleus 19782
                atom 19782
                  main group element atom 19670
                    p-block element atom 19670
                      carbon group element atom 19572
                        carbon atom 19561
                          organic molecular entity 19561
                            organic group 18493
                              organic divalent group 18486
                                organodiyl group 18486
                                  carbonyl group 18389
                                    carbonyl compound 18389
                                      carboxylic acid 18060
                                        carboacyl group 17346
                                          univalent carboacyl group 17346
                                            carbamoyl group 17132
                                              carboxamide 17132
                                                peptide 9391
                                                  depsipeptide 356
                                                    cyclodepsipeptide 337
                                                      romidepsin 43
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