⬤ Hydrogen (H): white
⬤ Carbon (C): gray
⬤ Oxygen (O): red
⬤ Phosphorus (P): orange
⬤ Nitrogen (N): blue
⬤ Selenium (Se): gold
⬤ Sulfur (S): yellow
Summary
| Full name | [(2R,3S,5S)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methyl dihydrogen phosphate |
| Short name | D2C |
| MODOMICS code | 1000000551G |
| Nature of the modified residue | Unnatural |
| RNAMods code | 仩 |
| Residue unique ID | 451 |
| Found in RNA | Yes |
Chemical information
| Sum formula | C9H14N3O7P |
| Type of moiety | nucleotide |
| SMILES | C1[C@@H]([C@H](O[C@@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O |
| logP | None |
| TPSA | None |
| Number of atoms | None |
| Number of Hydrogen Bond Acceptors 1 (HBA1) | None |
| Number of Hydrogen Bond Acceptors 2 (HBA2) | None |
| Number of Hydrogen Bond Donors (HBD) | None |
| InChI | InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8-/m0/s1 |
| InChIKey | NCMVOABPESMRCP-BBVRLYRLSA-N |
| Search the molecule in external databases | ChEMBL PubChem Compound Database Ligand Expo WIPO |
* Chemical properties calculated with Open Babel - O'Boyle et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011) (link)
QM Data:
| Dipole Magnitude [D]: | 7.713724577 |
| Energy [Eh]: | -1383.1997816763 |
| HOMO [eV]: | -9.1493 |
| LUMO [eV]: | 1.0399 |
| Gap [eV]: | 10.1892 |
Download QM Data:
| Charges | charge.txt |
Download Structures
| 2D | .png .mol .mol2 .sdf .pdb |
| 3D | .mol .mol2 .sdf .pdb |
Tautomers
| Tautomers SMILES |
[O-]P([O-])(=O)OCC1C(O)CC(n2ccc(=N)[nH]c2=O)O1 tautomer #0
[O-]P([O-])(=O)OCC1C(O)CC(n2ccc(N)nc2=O)O1 tautomer #1 [O-]P([O-])(=O)OCC1C(O)CC(n2ccc(=N)nc2O)O1 tautomer #2 |
| Tautomer image | Show Image |
LC-MS Information
| Monoisotopic mass | None |
| Average mass | None |
| [M+H]+ | not available |
| Product ions | not available |
| 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.
Last modification of this entry: Sept. 15, 2025