Summary

Full name3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine
IUPAC name2-amino-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxo-1,3-diazinan-1-yl]butanoic acid
Short nameacp3D
MODOMICS code308U
Synonyms
3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine
acp(3)D
CHEBI:71588
Q27139734
SCHEMBL18740452

Nature of the modified residueNatural
RNAMods codeÐ
Residue unique ID137
Found in RNAYes
Related nucleotides381
Found naturally in RNA typestRNA

Chemical information

Sum formulaC13H21N3O8
Type of moietynucleoside
Degeneracynot applicable
SMILESNC(CCN1C(=O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)CCC1=O)C(O)=O
logP-2.5422
TPSA173.86
Number of atoms24
Number of Hydrogen Bond Acceptors 1 (HBA1)11
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 5HT
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000497
InChIInChI=1S/C13H21N3O8/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/h6-7,9-11,17,19-20H,1-5,14H2,(H,21,22)/t6?,7-,9-,10-,11-/m1/s1
InChIKeyVBRZFUQRBSFADN-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)CC=C1O)C(=O)O tautomer #3
N=C(CCN1C(=O)N(C2OC(CO)C(O)C2O)CC=C1O)C(O)O tautomer #4
NC(=CCN1C(=O)N(C2OC(CO)C(O)C2O)CC=C1O)C(O)O tautomer #5
NC(CCN1C(=O)N(C2OC(CO)C(O)C2O)CCC1=O)=C(O)O tautomer #6
NC(CCN1C(=O)N(C2OC(CO)C(O)C2O)CC=C1O)=C(O)O tautomer #7

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
acp3D acp3D acp3D

* 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 mass347.1329
Average mass347.321
[M+H]+348.1407
Product ions216
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.

Chemical groups contained

TypeSubtype
aminoacyl groupaspartyl

Reactions producing 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine

Name
D:acp3D

Publications

Title Authors Journal Details PubMed Id DOI
3-(3-amino-3-carboxypropyl)-5,6-Dihydrouridine is one of two novel post-transcriptional modifications in tRNA(Lys) (UUU) from Trypanosoma brucei. Krog JS, Espanol Y, Giessing AM, Dziergowska A, Malkiewicz A, Ribas de Pouplana L, Kirpekar F FEBS J [details] 22040320 -

Last modification of this entry: Sept. 29, 2021


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