NP-MRD: Showing NP-Card for Cytidine 5'-(dihydrogen phosphate) (NP0333945)

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Record Information

Version

2.0

Created at

2024-09-09 21:22:40 UTC

Updated at

2024-09-09 21:22:41 UTC

NP-MRD ID

NP0333945

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytidine 5'-(dihydrogen phosphate)

Description

Isolated from biol. Sources, e.G. Phaseolus aureus (mung bean) seedlings Cytidine monophosphate is an ester of phosphoric acid with the nucleoside cytidine; it is a nucleotide found in RNA.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05242323542D          

 21 22  0  0  0  0            999 V2000
   -3.5251   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0401    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6744   -1.6491    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3690   -1.0679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4248    0.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0636   -0.4867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    5.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2172    4.3527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4328    4.3527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    3.5277    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    4.3527    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  5  1  0  0  0  0
  2 12  1  0  0  0  0
  3  4  1  0  0  0  0
  3 19  1  0  0  0  0
  4  6  1  0  0  0  0
  4 20  1  0  0  0  0
  5 10  2  0  0  0  0
  5 11  1  0  0  0  0
  6  7  1  0  0  0  0
  6 13  1  0  0  0  0
  7  8  1  0  0  0  0
  7 14  1  0  0  0  0
  8 12  1  0  0  0  0
  8 20  1  0  0  0  0
  9 11  2  0  0  0  0
  9 12  1  0  0  0  0
  9 15  1  0  0  0  0
 16 21  1  0  0  0  0
 17 21  1  0  0  0  0
 18 21  2  0  0  0  0
 19 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333945

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(O)C(OC1COP(O)(O)=O)N1C=CC(=N)N=C1O

> <INCHI_IDENTIFIER>
InChI=1/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)

> <INCHI_KEY>
IERHLVCPSMICTF-UHFFFAOYNA-N

> <FORMULA>
C9H14N3O8P

> <MOLECULAR_WEIGHT>
323.198

> <EXACT_MASS>
323.051851421

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
27.029867431418957

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid

> <JCHEM_LOGP>
-2.0358889072593436

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.694229434967237

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2213448807231149

> <JCHEM_PKA_STRONGEST_BASIC>
3.246548605172328

> <JCHEM_POLAR_SURFACE_AREA>
176.13

> <JCHEM_REFRACTIVITY>
76.83020000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-MAY-23         0                                  
HETATM    1  C   UNK     0      -6.580  -0.426   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.675   0.820   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.468   5.815   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.954  -1.832   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.698   1.905   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.238   1.905   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.517  -0.748   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -6.859  -3.078   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0      -4.422  -1.993   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -4.143   0.659   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       0.242   3.846   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -0.793   0.659   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -1.985  -0.909   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.134   9.665   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.406   8.125   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -2.674   8.125   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.134   6.585   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -3.714   3.370   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0      -1.134   8.125   0.000  0.00  0.00           P+0
CONECT    1    2    5                                                       
CONECT    2    1   12                                                       
CONECT    3    4   19                                                       
CONECT    4    3    6   20                                                  
CONECT    5    1   10   11                                                  
CONECT    6    4    7   13                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7   12   20                                                  
CONECT    9   11   12   15                                                  
CONECT   10    5                                                            
CONECT   11    5    9                                                       
CONECT   12    2    8    9                                                  
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    9                                                            
CONECT   16   21                                                            
CONECT   17   21                                                            
CONECT   18   21                                                            
CONECT   19    3   21                                                       
CONECT   20    4    8                                                       
CONECT   21   16   17   18   19                                             
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Value	Source
Cytidine 5'-(dihydrogen phosphoric acid)	Generator

Chemical Formula

C₉H₁₄N₃O₈P

Average Mass

323.1980 Da

Monoisotopic Mass

323.05185 Da

IUPAC Name

{[3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid

Traditional Name

[3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

OC1C(O)C(OC1COP(O)(O)=O)N1C=CC(=N)N=C1O

InChI Identifier

InChI=1/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)

InChI Key

IERHLVCPSMICTF-UHFFFAOYNA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Aminopyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Imidolactam
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
1,2-diol
Oxacycle
Organoheterocyclic compound
Azacycle
Organopnictogen compound
Amine
Alcohol
Organic oxide
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Primary amine
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2	ChemAxon
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	3.25	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	176.13 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	76.83 m³·mol⁻¹	ChemAxon
Polarizability	27.03 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cytidine 5'-(dihydrogen phosphate) (NP0333945)

MOL for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

3D MOL for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

3D SDF for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

3D-SDF for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

PDB for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

3D PDB for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

SMILES for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

INCHI for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

Structure for NP0333945 (Cytidine 5'-(dihydrogen phosphate))

3D Structure for NP0333945 (Cytidine 5'-(dihydrogen phosphate))