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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 4:25,357,467...25,529,941
Ensembl chr 4:25,158,362...25,442,709
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 chr10:528,961...655,179
Ensembl chr10:531,812...655,114
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 6:131,713,716...131,735,319
Ensembl chr 6:131,713,720...131,733,921
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 chr20:5,100,480...5,109,669
Ensembl chr20:5,100,480...5,109,264
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 8:89,716,914...89,724,998
Ensembl chr 8:89,716,914...89,724,998
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 3:141,253,508...141,304,582
Ensembl chr 3:141,253,523...141,303,479
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 3:115,366,783...115,404,068
Ensembl chr 3:115,366,646...115,404,068
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 3:96,165,042...96,215,621
Ensembl chr 3:96,165,042...96,215,615
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 8:4,968,856...4,989,325
Ensembl chr 8:4,968,842...4,988,732
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 chr10:103,072,530...103,081,382
Ensembl chr10:103,073,408...103,081,380
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 chr16:45,662,910...45,681,171
Ensembl chr16:45,662,910...45,684,648
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 5:154,108,872...154,126,628
Ensembl chr 5:154,109,046...154,126,626
JBrowse link
G Ccna2 cyclin A2 decreases expression ISO romidepsin results in decreased expression of CCNA2 protein CTD PMID:15014036 NCBI chr 2:119,427,239...119,433,645
Ensembl chr 2:119,426,089...119,433,577
JBrowse link
G Ccnb1 cyclin B1 decreases expression ISO romidepsin results in decreased expression of CCNB1 protein CTD PMID:15014036 NCBI chr 2:31,912,190...31,921,163
Ensembl chr 2:31,912,193...31,921,172
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 chr20:7,149,177...7,159,727
Ensembl chr20:7,149,217...7,159,585
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 9:60,185,338...60,236,173
Ensembl chr 9:60,185,452...60,237,034
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 8:58,096,021...58,102,130
Ensembl chr 8:58,096,077...58,102,125
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 1:81,652,762...81,732,153
Ensembl chr 1:81,652,787...81,732,143
JBrowse link
G Cyp3a2 cytochrome P450, family 3, subfamily a, polypeptide 2 affects metabolic processing ISO CYP3A4 protein affects the metabolism of romidepsin CTD PMID:15635176 NCBI chr12:9,207,986...9,230,038
Ensembl chr12:9,015,383...9,285,008
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 chr12:16,806,222...16,846,428
Ensembl chr12:16,806,207...16,846,422
JBrowse link
G Egfr epidermal growth factor receptor decreases expression ISO romidepsin results in decreased expression of EGFR protein CTD PMID:15014036 NCBI chr14:91,176,931...91,349,722
Ensembl chr14:91,177,067...91,344,382
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 chr10:83,411,197...83,435,078
Ensembl chr10:83,411,313...83,435,078
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 chr14:79,965,365...79,994,108
Ensembl chr14:79,965,368...79,994,544
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 8:30,831,422...30,950,468
Ensembl chr 8:30,832,753...30,950,433
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 1:156,200,044...156,218,380
Ensembl chr 1:156,200,060...156,205,724
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 8:44,671,927...44,673,257
Ensembl chr 8:44,671,786...44,673,239
JBrowse link
G H3f4 H3.4 histone increases acetylation ISO romidepsin results in increased acetylation of H3-4 protein CTD PMID:16006969 NCBI chr10:43,740,797...43,741,207 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 chr20:40,548,250...40,571,609
Ensembl chr20:40,548,250...40,571,609
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 6:92,624,059...92,669,262
Ensembl chr 6:92,624,390...92,669,261
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 8:19,553,063...19,565,438
Ensembl chr 8:19,553,645...19,565,438
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 chr11:83,957,813...84,023,629
Ensembl chr11:83,957,813...84,023,616
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 1:181,366,646...181,372,863
Ensembl chr 1:181,366,637...181,372,863
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 2:183,219,137...183,235,676
Ensembl chr 2:183,219,220...183,222,303
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 2:224,016,214...224,132,135
Ensembl chr 2:224,016,214...224,110,404
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 6:72,858,713...72,861,941
Ensembl chr 6:72,858,712...72,861,941
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 chr13:83,632,940...83,638,193
Ensembl chr13:83,632,899...83,637,906
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 chr13:92,307,593...92,339,406
Ensembl chr13:92,307,586...92,339,404
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 3:19,584,015...19,605,589
Ensembl chr 3:19,584,015...19,605,586
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 4:148,679,534...148,740,265
Ensembl chr 4:148,679,530...148,740,317
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 chr15:48,371,295...48,502,473
Ensembl chr15:48,371,296...48,502,302
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 1:202,925,001...202,935,484
Ensembl chr 1:202,924,945...202,935,484
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 3:89,005,129...89,126,498
Ensembl chr 3:89,005,129...89,126,498
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 9:14,955,300...14,970,641
Ensembl chr 9:14,955,300...14,970,641
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:120,890,537...120,938,413
Ensembl chr  X:120,897,907...120,934,700
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  CHEBI ontology 19812
    role 19761
      biological role 19761
        antimicrobial agent 17400
          heterocyclic antibiotic 1637
            romidepsin 44
Path 2
Term Annotations click to browse term
  CHEBI ontology 19812
    subatomic particle 19811
      composite particle 19811
        hadron 19811
          baryon 19811
            nucleon 19811
              atomic nucleus 19811
                atom 19811
                  main group element atom 19708
                    p-block element atom 19708
                      carbon group element atom 19630
                        carbon atom 19620
                          organic molecular entity 19620
                            organic group 18728
                              organic divalent group 18719
                                organodiyl group 18719
                                  carbonyl group 18667
                                    carbonyl compound 18667
                                      carboxylic acid 18364
                                        carboacyl group 17482
                                          univalent carboacyl group 17482
                                            carbamoyl group 17298
                                              carboxamide 17298
                                                peptide 9444
                                                  depsipeptide 356
                                                    cyclodepsipeptide 337
                                                      romidepsin 44
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