Modomics - A Database of RNA Modifications

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 name	N4-acetylcytidine
IUPAC name	N-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxopyrimidin-4-yl]acetamide
Short name	ac4C
MODOMICS code new	2000000042C
MODOMICS code	42C
Synonyms	3597-45-3 3768-18-1 4-[(1-Hydroxyethylidene)amino]-1-pentofuranosylpyrimidin-2(1H)-one 4-Acetyl-1-(beta-delta-ribofuranosyl)cytosine 4-Acetyl-1-(beta-D-ribofuranosyl)cytosine 4-Acetylcytidine 4-N-acetyl-cytidine 768A181 AC1L326V AC1Q5JLE AC-32170 Acetamide, N-(1,2-dihydro-2-oxo-1-beta-D-ribofuranosyl-4-pyrimidinyl) Acetamide, N-(1,2-dihydro-2-oxo-1-.beta.-D-ribofuranosyl-4-pyrimidinyl)- acetyl cytosine Acetylcytidine AJ-50600 AKOS015896940 AN-20958 AR-1K5740 AS-12329 C11-H15-N3-O6 C11H15N3O6 C22293 CA-237 CHEBI:70989 CID107461 CJ-11922 CS-0030784 CTK1C3669 Cytidine, N-acetyl- DTXSID40958718 EINECS 223-195-6 HY-W019670 K-8298 MFCD00006540 N-{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxo-1,2-dihydropyrimidin-4-yl}acetamide N-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxopyrimidin-4-yl]acetamide N-(1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-2-oxo-1,2-dihydropyrimidin-4-yl)acetamide N-{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-2-oxo-1,2-dihydropyrimidin-4-yl}acetamide N-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-2-oxo-pyrimidin-4-yl]acetamide N4 -Acetylcytidine n4-acetyl cytidine N-4-Acetylcytidine N4-Acetylcytidine n(4)-acetylcytidine N4-Acetylcytidine, 97.5% - 1G 1g N4-Acetylcytidine, >=98% n4-Acetylcytidine;n-acetylcytidine n-acetyl-Cytidine N-Acetylcytidine NIDVTARKFBZMOT-PEBGCTIMSA-N NS00014881 Q20890503 RT-001601 SC-09055 SCHEMBL453447 ST2419678 TL8002770 ZINC4321512
Nature of the modified residue	Natural
RNAMods code	M
Residue unique ID	81
Found in RNA	Yes
Related nucleotides	200
Enzymes	NAT10 (Homo sapiens) Rra1 (Saccharomyces cerevisiae) TmcA (Escherichia coli)
Found in phylogeny	Eubacteria, Eukaryota
Found naturally in RNA types	rRNA, tRNA

Chemical information

Sum formula	C11H15N3O6
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	CC(Nc1nc(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)cc1)=O
logP	-2.1138
TPSA	133.91
Number of atoms	20
Number of Hydrogen Bond Acceptors 1 (HBA1)	8
Number of Hydrogen Bond Acceptors 2 (HBA2)	9
Number of Hydrogen Bond Donors (HBD)	4
PDB no exac match , link to the most similar ligand	4AC
HMDB (Human Metabolome Database) exact match	None
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand	None
InChI	InChI=1S/C11H15N3O6/c1-5(16)12-7-2-3-14(11(19)13-7)10-9(18)8(17)6(4-15)20-10/h2-3,6,8-10,15,17-18H,4H2,1H3,(H,12,13,16,19)/t6-,8-,9-,10-/m1/s1
InChIKey	NIDVTARKFBZMOT-PEBGCTIMSA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	107461
PubChem SIDs	3259595 10234296 15047006 24891274 44436504 49832701 75499853 85257106 89744260 103839939 104379012 117570010 126675178 128705906 135063459 135684809 140033841 143178688 152036359 160646142 162174992 162225930 162516973 184819159 204364817 223497276 223559771 223669059 224430192 226773627 249716391 249839719 250214780 251897802 252228349 252316684 252354262 252400619 252411664 252452559 253666544 255437480 257237187 273528943 275918858 310265507 312226908 312595118 315445664 318050073 319138785 319450154 321933960 322082121 329864972 340563856 341251339 341837340 342526826 346699370 347797336 348276786 349017553 350078846 354266649 363671310 373739268 374046241 374171812 375136892 375556673 375668547 375736649 376152865 381013522 381374964 382370911 383452029 384515736 385647742 386484148 387128589 403600999 404623074 404826326 405111379 406168202 406529169 406675444 419541135 433774500 433774889 433775453 433840436 434384512 438515913 439455783 440703668 441087788 441133466 443523017

^* 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	CC(N=c1[nH]c(=O)n(C2C(O)C(O)C(CO)O2)cc1)=O tautomer #0 CC(Nc1nc(=O)n(C2C(O)C(O)C(CO)O2)cc1)=O tautomer #1 C=C(N=c1[nH]c(=O)n(C2C(O)C(O)C(CO)O2)cc1)O tautomer #2 C=C(Nc1nc(=O)n(C2C(O)C(O)C(CO)O2)cc1)O tautomer #3 CC(N=c1nc(O)n(C2C(O)C(O)C(CO)O2)cc1)=O tautomer #4 CC(=Nc1nc(=O)n(C2C(O)C(O)C(CO)O2)cc1)O tautomer #5 C=C(N=c1nc(O)n(C2C(O)C(O)C(CO)O2)cc1)O tautomer #6
Tautomer image	Show Image

Predicted CYP Metabolic Sites

CYP3A4	CYP2D6	CYP2C9

^* 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 mass	285.0961
Average mass	285.253
[M+H]⁺	286.1039
Product ions	154/112
Normalized LC elution time^*	1,35 (Kellner 2014)
LC elution order/characteristics	between G and A (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	-
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers.	Kellner S, Ochel A, Thuring K, Spenkuch F, Neumann J, Sharma S, Entian KD, Schneider D, Helm M...	Nucleic Acids Res	[details]	25129236	-

Chemical groups contained

Type	Subtype
other	acetylamide

Reactions producing N4-acetylcytidine

Name
C:ac4C

Reactions starting from N4-acetylcytidine

Name
ac4C:ac4Cm

Last modification of this entry: Sept. 22, 2023