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	adenosine
IUPAC name	(2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol
Short name	A
MODOMICS code new	A
MODOMICS code	A
Nature of the modified residue	Natural
RNAMods code	A
Residue unique ID	109
Found in RNA	Yes
Related nucleotides	444
Enzymes	ALKBH5 (Homo sapiens) FTO (Homo sapiens) ALKBH3 (Homo sapiens)
Found in phylogeny	Archaea, Eubacteria, Eukaryota

Chemical information

Sum formula	C10H13N5O4
Type of moiety	nucleoside
Degeneracy	not applicable
PubChem ID	60961
SMILES	Nc1ncnc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
logP	-1.3988
TPSA	139.54
Number of atoms	19
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	ADN
PDB exact match , link to the most similar ligand	ADN
HMDB (Human Metabolome Database) exact match	None
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand	None
InChI	InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
InChIKey	OIRDTQYFTABQOQ-KQYNXXCUSA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	60961
PubChem SIDs	2103 3512 584484 584490 585862 586357 597013 819854 821994 823447 825728 826920 828107 828519 829493 830178 830391 833174 833907 836875 837192 855078 855932 3136392 7847113 7885717 7978645 8023217 8024149 8027268 8143428 8187141 10318629 11110168 11120317 11120805 11121293 11371396 11484930 11489073 11490104 11532406 11532673 11537606 14716094 14774851 14799162 22394812 24277685 24698217 24875177 24890739 26611593 26679885 26703421 26718521 26746554 26751564 29196283 29196284 30894316 43118274 46392770 46394143 46394193 46394457 46484664 46508728 47170007 47885198 48415518 49655269 49655272 49833639 49865053 50104175 50104176 50104177 53776935 53789432 56436529 56462979 56479554 57314201 57410855 76747733 81044335 81044589 81060289 81061992 81067306 81067308 85164908 85747823 85856093 87235637 87235640 87235942 87561839 88881212 89449259 90341699 92092948 92123937 92297858 92307323 92708890 93578298 99205913 99206458 99213397 99213399 99344330 103059163 103168984 104234127 104322053 113585170 117358470 117529572 121360335 124511102 124636671 124801154 124807074 124807076 125011540 125317120 126531873 126610610 126617407 126648007 127710303 128808466 128814610 131349748 134419356 134419362 134465061 134465064 135017562 135023145 135363564 135651426 135697784 136905477 141402135 144074868 144087463 144187457 144204442 144220196 144223831 152028013 152146256 152165809 152199007 152199380 152199382 152213583 152246918 152255846 160644256 160644269 160644360 160644365 160654810 160661732 160800495 160963315 160963985 162010594 162010596 162164611 162164615 162164620 162164624 162175872 162546793 163309936 163309940 163309946 163309951 163309956 163309961 163309965 163309968 163309992 163632141 163632144 163632148 163632159 163805454 164187596 165235234 166223213 170465447 170481835 170482051 170482052 172088298 172096945 172097241 172818588 172818589 174476339 174560556 174560557 174861394 175267213 175442864 176484723 177900177 179116545 186014033 188627610 191112141 196679231 196679566 202542071 203105347 203105348 203355603 204380690 204938556 208011837 223399178 223448740 223448741 223448742 223493278 223543191 223704315 223755620 226393686 241102165 241107868 247624603 249828367 250014044 250204756 252091259 252157410 252165751 252166360 252214665 252300428 252344734 252344987 252400620 252401514 252403306 252452542 252824089 252824132 253663270 254761250 254761332 254801280 255386300 256401226 268734441 274086925 274951514 303072568 310262719 310262720 310263432 310265846 310265851 312225583 312523915 312695155 313076412 313080027 315668832 315668992 315673253 316392295 316892278 316892387 316892465 316892485 316900015 316905706 316919279 316920853 318151261 318151333 318160125 318172011 318344231 318464677 319102634 319102635 319102636 319459022 319886569 321934527 321949256 329591786 329731594 329747369 329748939 329770589 329823158 329824924 329829826 329847636 329847645 329847648 329973333 332875215 333494164 335039484 335990978 336285802 336285814 336286130 336295724 336943743 336943750 340081489 340088020 340098021 340470201 340471899 340515918 340555819 341139553 341199320 342526847 342580114 342582262 346400971 346693934 347758307 347831535 347912820 348274216 348355314 348355335 348355337 348438242 348479486 349140889 349980556 350088991 354266903 354302978 354332844 354349517 354349522 354349561 354349918 354350051 354702003 354702835 354974439 355159480 355199160 363321572 363593955 363900507 374017305 374168415 374364854 374403762 375079260 375134796 375136880 375555980 375573931 375573940 375574172 375635747 375684060 375983892 375984679 376011197 376152558 376163210 376171060 376171061 376171062 376171063 376195395 376219337 376227683 376353068 376860644 381000614 381007165 381025204 381117629 381119384 381119394 381119410 381133238 381327550 381364967 381647123 382372209 383147010 383470907 383861765 384256138 384405291 384568019 384571763 384653561 385147651 385153749 385645894 385793543 385980684 386045133 386187122 386294462 386466681 386482264 387021983 387060785 387133616 402316079 403033267 404418611 404721170 404748957 404758245 404827251 405041252 405057369 405057460 405231790 405558447 406183991 406514612 406800471 406800478 406842608 419507710 433774918 433776075 433776350 433776728 433776963 433777176 433777177 433777178 433777767 433780475 434131521 434139460 434293470 434295111 434482682 438444695 438474521 438474522 438505462 438568470 438630681 438652168 439442453 439593665 439641179 440064758 440076373 440787271 440790669 441087793 441119028 441294525 441562671 441579649 441654170 441657075 441657697 443507703 443534131 443534133 443548334 443623779

^* 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	Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O tautomer #0 Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O tautomer #1 N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O tautomer #2 N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O tautomer #3 N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O tautomer #4
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	267.0968
Average mass	267.241
[M+H]⁺	268.1046
Product ions	136
Normalized LC elution time^*	1.43
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 producing adenosine

Name
m6A:A
m1A:A

Reactions starting from adenosine

Name
A:t6A
A:hn6A
A:I
A:m6A
A:m1A
A:g6A
A:i6A
A:Am
A:m2A
A:Ar(p)
A:m8A

Last modification of this entry: Oct. 19, 2023