Summary

Full namecytidine
IUPAC name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
Short nameC
MODOMICS codeC
Synonyms
111398-92-6
14419-78-4
147-94-4
16501-EP2281563A1
16501-EP2287165A2
16501-EP2287166A2
16501-EP2289892A1
16501-EP2292088A1
16501-EP2292620A2
16501-EP2292630A1
16501-EP2295407A1
16501-EP2298736A1
16501-EP2298783A1
16501-EP2305808A1
16501-EP2316459A1
185553-94-0
1beta-2'-Ribofuranosylcytosine, d-
1-Beta-d-ribofuranoside cytosine
1-(beta-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
1-(beta-D-ribofuranosyl)-4-aminopyrimidin-2-one
1-beta-D-Ribofuranosylcytosine
1.beta.-D-Ribofuranosylcytosine
1beta-D-Ribofuranosylcytosine
1-beta-D-ribosyl- (6CI)
1-beta-Ribofuranosylcytosine
1.beta.-Ribofuranosylcytosine
1beta-Ribofuranosylcytosine
2(1H)-Pyrimidinone, 4-amino-1-beta-D-ribofuranosyl-
2(1H)-Pyrimidinone, 4-amino-1-.beta.-D-ribofuranosyl-
2(1H)-Pyrimidinone, 4-amino-1beta-D-ribofuranosyl-
32747-18-5
3h-cytidine
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2-one
4-Amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone
4-Amino-1-beta-D-ribofuranosyl-2-(1H)-pyrimidinone
4-Amino-1.beta.-D-ribofuranosyl-2(1H)-pyrimidinone
4-Amino-1-.beta.-D-ribofuranosyl-2-(1H)-pyrimidinone
4-Amino-1beta-D-ribofuranosyl-2(1H)-pyrimidinone
4-amino-1-beta-D-ribofuranosylpyrimidin-2(1H)-one
5CSZ8459RP
6018-48-0
65-46-3
65C463
67875-14-3
6D2DC474-DD76-4081-8B34-10605C218F49
AB0012341
AC1L1LY9
AC1Q6C2P
ACN-047006
AJ-43263
AKOS015888568
AM83932
AN-23747
ANW-35046
AR-1I3421
AS-12696
BC679398
beta-cytidine
beta.-D-Ribo-C
.beta.-D-Ribofuranoside, cytosine-1
beta-D-Ribofuranoside, cytosine-1
beta-D-ribofuranosyl-cytidine
bmse000190
bmse000969
bmse001020
BRD-K71847383-001-12-5
C00475
c0522
C9-H13-N3-O5
C9H13N3O5
CCG-266896
CHEBI:17562
CHEMBL95606
CID6175
CJ-10310
CP-C
CS-1989
CTK2F3027
CTN
Cyd
CYT007
cytarabine
cytidin-
Cytidin
cytidine
Cytidine-
Cytidine, 99%
Cytidine, 99+%
Cytidine, 99% - 100g 100g
Cytidine 99% for biochemistry 1gm
Cytidine, >=99.0% (HPLC)
Cytidine, BioReagent, suitable for cell culture, powder, >=99%
cytidine, N-15N-
cytidine-2'-13C
Cytidine-5'-monophosphate
cytosine
Cytosine, 1-beta-D-ribofuranosyl-
Cytosine, 1-.beta.-D-ribofuranosyl-
Cytosine beta-D-riboside
Cytosine Ribonucleoside
Cytosine riboside
Cytosine-1-beta-D-ribofuranoside
cytosine-1beta-D-Ribofuranoside
Cytosine-1-??-D-ribofuranoside
D003562
D07769
D0E7ES
DB02097
DB-029614
DTXSID60891552
EINECS 200-610-9
Epitope ID:141494
ERK5-5D16
F0348-2240
GTPL4728
HY-B0158
I14-8299
J-700167
KM0929
KSC353A2P
LS-135845
MCULE-3044641322
MFCD00006545
MLS000049947
MLS002207040
MMV638723
NCGC00093356-08
NCGC00142483-01
NCGC00142483-09
NS00069068
NSC 20258
NSC-20258
Posilent (TN)
PubChem14146
Q422538
Ribonucleoside, Cytosine
Riboside, Cytosine
RTR-022281
s2053
SBB003195
SC-09086
SCHEMBL7179
SMR000058243
SRI-2352_17
ST056938
ST24046405
TL8004649
TR-022281
UHDGCWIWMRVCDJ-XVFCMESISA-N
UNII-5CSZ8459RP
UNII-F2 component UHDGCWIWMRVCDJ-XVFCMESISA-N
ZINC2583632
Zytidin

Nature of the modified residueNatural
RNAMods codeC
Residue unique ID46
Found in RNAYes
Related nucleotides300
Found in phylogenyArchaea, Eubacteria, Eukaryota

Chemical information

Sum formulaC9H13N3O5
Type of moietynucleoside
Degeneracynot applicable
PubChem ID6175
SMILESNc1nc(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)cc1
logP-1.9818
TPSA130.83
Number of atoms17
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand AR3
PDB exact match , link to the most similar ligand CTN
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000089
InChIInChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
InChIKeyUHDGCWIWMRVCDJ-XVFCMESISA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs
2561
3758
610624
833276
841097
3132638
8144101
8153876
11110524
15342347
24892387
24892710
26754267
29225173
46507502
49684259
49693276
49834502
50036797
51092061
56459360
76890969
81044585
85098495
85165010
85230757
87565639
88211484
92297505
93576752
99246698
99381411
99453898
103313321
103823300
104223697
104311310
117588066
124558522
125264648
126635400
127303743
127303744
127303745
127303746
127303747
127303748
127303749
127303750
127303751
127303752
127303753
127303754
127384931
129367679
134358227
134972626
135685795
135724043
141570606
143394255
143489900
144080970
152027987
152242426
160661250
160802547
160963339
162038205
162175968
162630232
163426397
163632145
163716059
163805987
166277333
170474753
172088432
172107065
173906049
174007401
174315350
175442899
178101439
179292990
186003633
196109816
196679569
198957111
198993689
202549302
204376863
204938834
210279274
210281597
223375013
223495664
223552434
223677776
223792907
226398597
241113098
249865593
249983031
250211078
251884734
252163455
252363789
252402910
252447775
252452543
254761563
256572846
274087254
274953939
297479397
310270773
312225602
312343811
312601946
312695378
313080572
315341612
316395223
316892546
316892729
316921192
316966583
318240869
318488409
318590545
319064183
319489182
319554757
319882380
319890062
321934797
322059271
322077169
329753447
340080859
340124212
340135615
340520856
340522511
341141448
341154419
341832268
342526823
346712608
347831235
347913432
348397209
349218412
349986179
350089009
354266931
354304556
354702859
355038901
363603463
369356365
374128468
374168594
374403272
375136881
375190369
375556233
375670225
376152681
376164834
376164835
376164836
376195058
376242158
376419765
376430816
381001234
381006387
381028160
381330211
383215893
384417744
384444706
384568164
384571950
385784959
385862969
385877179
385915098
385980678
386265492
386621873
387159318
403400724
403830282
404753699
404755352
404827682
405025590
405133338
405558808
406184055
406514670
406774413
419527583
433775069
433776956
433777277
433777278
433777842
433780615
434700782
438515810
439591713
439641553
440065247
440076377
440822629
441028421
441087776
441295793
441556482
443549517
443623778

* 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
N=c1[nH]c(=O)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #0
Nc1nc(=O)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #1
N=c1nc(O)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
C C C

* 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 mass243.0855
Average mass243.217
[M+H]+244.0933
Product ions112
Normalized LC elution time *0.42
LC elution order/characteristics not available

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

Reactions starting from cytidine

Name
C:k2C
C:ac4C
C:m3C
C:f5C
C:Cm
C:m4C
C:m5C
C:hm5C
C:s2C
C:U
C:C+
C:ho5C

Last modification of this entry: Sept. 29, 2021


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