Modomics - A Database of RNA Modifications

acp3Y
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)pseudouridine
IUPAC name2-amino-4-[5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxo-1H-pyrimidin-3-yl]butanoic acid
Short nameacp3Y
MODOMICS code new2000000309U
MODOMICS code309U
Synonyms
2-amino-4-[5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxo-1H-pyrimidin-3-yl]butanoic acid
SCHEMBL2751846
Nature of the modified residueNatural
RNAMods codeÞ
Residue unique ID138
Found in RNAYes
Related nucleotides348

Chemical information

Sum formulaC13H19N3O8
Type of moietynucleoside
Degeneracynot applicable
SMILESNC(C(=O)O)CC[n]1c(=O)c([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c[nH]c1=O
logP-2.8071
TPSA188.1
Number of atoms24
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)10
Number of Hydrogen Bond Donors (HBD)6
PDB no exac match , link to the most similar ligand B8N
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C13H19N3O8/c14-6(12(21)22)1-2-16-11(20)5(3-15-13(16)23)10-9(19)8(18)7(4-17)24-10/h3,6-10,17-19H,1-2,4,14H2,(H,15,23)(H,21,22)/t6?,7-,8-,9-,10+/m1/s1
InChIKeyZHENYVBBFCVMEV-BKLVVQOLSA-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(C(O)=O)CCN1C(=O)C(C2C(O)C(O)C(CO)O2)C=NC1=O tautomer #0
N=C(C(O)O)CCN1C(=O)C(C2C(O)C(O)C(CO)O2)C=NC1=O tautomer #1
NC(C(O)=O)CCn1c(=O)c(C2C(O)C(O)C(CO)O2)c[nH]c1=O tautomer #2
N=C(C(O)O)CCn1c(=O)c(C2C(O)C(O)C(CO)O2)c[nH]c1=O tautomer #3
NC(C(O)O)=CCN1C(=O)C(C2C(O)C(O)C(CO)O2)C=NC1=O tautomer #4
NC(C(O)O)=CCn1c(=O)c(C2C(O)C(O)C(CO)O2)c[nH]c1=O tautomer #5
NC(C(O)=O)CCn1c(O)c(C2C(O)C(O)C(CO)O2)cnc1=O tautomer #6
N=C(C(O)O)CCn1c(O)c(C2C(O)C(O)C(CO)O2)cnc1=O tautomer #7
NC(C(O)O)=CCn1c(O)c(C2C(O)C(O)C(CO)O2)cnc1=O tautomer #8
NC(=C(O)O)CCN1C(=O)C(C2C(O)C(O)C(CO)O2)C=NC1=O tautomer #9
NC(C(O)=O)CCn1c(=O)c(C2C(O)C(O)C(CO)O2)cnc1O tautomer #10
N=C(C(O)O)CCn1c(=O)c(C2C(O)C(O)C(CO)O2)cnc1O tautomer #11
NC(=C(O)O)CCn1c(=O)c(C2C(O)C(O)C(CO)O2)c[nH]c1=O tautomer #12
NC(C(O)O)=CCn1c(=O)c(C2C(O)C(O)C(CO)O2)cnc1O tautomer #13
NC(=C(O)O)CCn1c(O)c(C2C(O)C(O)C(CO)O2)cnc1=O tautomer #14
NC(=C(O)O)CCn1c(=O)c(C2C(O)C(O)C(CO)O2)cnc1O tautomer #15
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
acp3Y acp3Y acp3Y

* 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
Normalized LC elution time * not available
LC elution order/characteristics not available

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

Comments

acp3Y is accumulated when the Nep1 enzyme is absent. The enzyme catalyzing the acp3Y formation in S. cerevisiae is still unknown.

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

Name
Y:acp3Y
acp3U:acp3Y

Publications

Title Authors Journal Details PubMed Id DOI
The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Psi1191 in yeast 18S rRNA. Meyer B, Wurm JP, Kotter P, Leisegang MS, Schilling V, Buchhaupt M, Held M, Bahr U, Karas M, Heckel A, Bohnsack MT, Wohnert J, Entian KD Nucleic Acids Res [details] 20972225 -

Last modification of this entry: Sept. 22, 2023