Modomics - A Database of RNA Modifications

acp3U
The molecule is shown in a ball-and-stick representation with the following colors for atoms :
⬤ Hydrogen (H): white ⬤ Carbon (C): gray ⬤ Oxygen (O): red ⬤ Phosphorus (P): orange ⬤ Nitrogen (N): blue ⬤ Selenium (Se): gold ⬤ Sulfur (S): yellow

Summary

Full name3-(3-amino-3-carboxypropyl)uridine
IUPAC name2-amino-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxopyrimidin-1-yl]butanoic acid
Short nameacp3U
MODOMICS code new2000000030U
MODOMICS code30U
Synonyms
1(2H)-Pyrimidinebutanoic acid, alpha-amino-3,6-dihydro-2,6-dioxo-3-beta-D-ribofuranosyl-
1(2H)-Pyrimidinebutanoicacid, a-amino-3,6-dihydro-2,6-dioxo-3-b-D-ribofuranosyl-
2-amino-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxopyrimidin-1-yl]butanoic acid
3-(3-Amino-3-carboxypropyl)-1-pentofuranosylpyrimidine-2,4(1H,3H)-dione
3-(3-Amino-3-carboxypropyl)uridine
3-(3-Carboxy-3-aminopropyl)uridine
52745-94-5
AC1L571Q
(acp(3))u
C13-H19-N3-O8
C13H19N3O8
CHEBI:19928
CID171198
CTK4J6422
DTXSID10967195
Nucleoside X
Q27109263
SCHEMBL440190
Nature of the modified residueNatural
RNAMods codeX
Residue unique ID75
Found in RNAYes
Related nucleotides382
Found naturally in RNA typesrRNA, tRNA

Chemical information

Sum formulaC13H19N3O8
Type of moietynucleoside
Degeneracynot applicable
SMILESNC(CC[n]1c(=O)[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)ccc1=O)C(O)=O
logP-2.8762
TPSA177.24
Number of atoms24
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)11
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand URI
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C13H19N3O8/c14-6(12(21)22)1-3-15-8(18)2-4-16(13(15)23)11-10(20)9(19)7(5-17)24-11/h2,4,6-7,9-11,17,19-20H,1,3,5,14H2,(H,21,22)/t6?,7-,9-,10-,11-/m1/s1
InChIKeyYXNIEZJFCGTDKV-JANFQQFMSA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs

* Chemical properties calculated with Open Babel - O'Boyle et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011) (link)


Download Structures

2D   .png .mol .mol2 .sdf .pdb .smi
3D   .mol .mol2 .sdf .pdb

Tautomers

Tautomers SMILES
NC(CCn1c(=O)n(C2OC(CO)C(O)C2O)ccc1=O)C(=O)O tautomer #0
N=C(CCn1c(=O)n(C2OC(CO)C(O)C2O)ccc1=O)C(O)O tautomer #1
NC(=CCn1c(=O)n(C2OC(CO)C(O)C2O)ccc1=O)C(O)O tautomer #2
NC(CCn1c(=O)n(C2OC(CO)C(O)C2O)ccc1=O)=C(O)O tautomer #3
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
acp3U acp3U acp3U

* CYP Metabolic sites predicted with SMARTCyp. SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450. It has been shown to be applicable to metabolism by the isoforms 1A2, 2A6, 2B6, 2C8, 2C19, 2E1, and 3A4 (CYP3A4), and specific models for the isoform 2C9 (CYP2C9) and isoform 2D6 (CYP2D6). CYP3A4, CYP2D6, and CYP2C9 are the three of the most important enzymes in drug metabolism since they are involved in the metabolism of more than half of the drugs used today. The three top-ranked atoms are highlighted. See: SmartCYP and SmartCYP - background; Patrik Rydberg, David E. Gloriam, Lars Olsen, The SMARTCyp cytochrome P450 metabolism prediction server, Bioinformatics, Volume 26, Issue 23, 1 December 2010, Pages 2988–2989 (link)


LC-MS Information

Monoisotopic mass345.1172
Average mass345.305
[M+H]+346.125
Product ions214/197/168
Normalized LC elution time *0,46 (Kellner 2014)
LC elution order/characteristicsbetween C and U (Kellner 2014)

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.


LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Profiling of RNA modifications by multiplexed stable isotope labelling. Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. Chem Commun (Camb). [details] 24567952 -

Chemical groups contained

TypeSubtype
aminoacyl groupaspartyl

Reactions producing 3-(3-amino-3-carboxypropyl)uridine

Name
U:acp3U

Reactions starting from 3-(3-amino-3-carboxypropyl)uridine

Name
acp3U:acp3Um
acp3U:acp3Y

Last modification of this entry: Sept. 22, 2023