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Showing NP-Card for Cytidine 5'-triphosphate (NP0333954)

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Record Information
Version2.0
Created at2024-09-09 21:24:55 UTC
Updated at2024-09-09 21:24:55 UTC
NP-MRD IDNP0333954
Secondary Accession NumbersNone
Natural Product Identification
Common NameCytidine 5'-triphosphate
DescriptionFound in cheese and liver CTP is a high-energy molecule equal to ATP, but its role in the organism is more specific than that of ATP. CTP is used as the source of energy, and as a coenzyme in metabolic reactions like the synthesis of glycerophospholipids and glycosylation of proteins.; CTP is a substrate in the synthesis of RNA.; Cytidine 5'-(tetrahydrogen triphosphate) or CTP is a cytosine nucleotide containing three phosphate groups esterified to a ribose moiety at the 5' position. CTP is integral to the synthesis or mRNA, rRNA and tRNA through RNA polymerases. Cytidine triphosphate (CTP) is also critical to the synthesis of phosphatidylcholine via the enzyme CTP: Phosphocholine cytidyltransferase. This reaction is the rate-limiting step in the synthesis of phosphatidylcholine.; Cytidine triphosphate is a pyrimidine nucleotide.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0333954 (Cytidine 5'-triphosphate)


  Mrv2104 05242323572D          

 29 30  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
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   -1.0636   -0.4867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.6078    4.3527    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
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  7 14  1  0  0  0  0
  8 12  1  0  0  0  0
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  9 11  2  0  0  0  0
  9 12  1  0  0  0  0
  9 15  1  0  0  0  0
 16 27  1  0  0  0  0
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 23 28  1  0  0  0  0
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 25 29  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
M  END
Download

3D MOL for NP0333954 (Cytidine 5'-triphosphate)

Download
3D SDF for NP0333954 (Cytidine 5'-triphosphate)

  Mrv2104 05242323572D          

 29 30  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
    0.8212    7.6527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6462    6.8277    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0038    6.8277    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
    0.5192    4.8757    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3058    6.3047    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
    0.8212    6.0027    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
    0.8212    6.8277    0.0000 P   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
    0.1067    5.5902    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 23  1  0  0  0  0
  4  6  1  0  0  0  0
  4 24  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 24  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 27  1  0  0  0  0
 17 27  1  0  0  0  0
 18 27  2  0  0  0  0
 19 28  1  0  0  0  0
 20 28  2  0  0  0  0
 21 29  1  0  0  0  0
 22 29  2  0  0  0  0
 23 28  1  0  0  0  0
 25 27  1  0  0  0  0
 25 29  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333954

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)

> <INCHI_KEY>
PCDQPRRSZKQHHS-UHFFFAOYNA-N

> <FORMULA>
C9H16N3O14P3

> <MOLECULAR_WEIGHT>
483.155

> <EXACT_MASS>
482.984513201

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
36.14149270737461

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <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}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid

> <JCHEM_LOGP>
-2.956043508264129

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.4562777359339467

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8933313089128676

> <JCHEM_PKA_STRONGEST_BASIC>
3.572613145668973

> <JCHEM_POLAR_SURFACE_AREA>
269.19

> <JCHEM_REFRACTIVITY>
98.57599999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
({[3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0333954 (Cytidine 5'-triphosphate)
Download
PDB for NP0333954 (Cytidine 5'-triphosphate)
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       1.533  14.285   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.073  12.745   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -0.007  12.745   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.406   8.125   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.674   8.125   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.969   9.101   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -0.571  11.769   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -1.134   6.585   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -3.714   3.370   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       1.533  11.205   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -1.134   9.665   0.000  0.00  0.00           O+0
HETATM   27  P   UNK     0       1.533  12.745   0.000  0.00  0.00           P+0
HETATM   28  P   UNK     0      -1.134   8.125   0.000  0.00  0.00           P+0
HETATM   29  P   UNK     0       0.199  10.435   0.000  0.00  0.00           P+0
CONECT    1    2    5                                                       
CONECT    2    1   12                                                       
CONECT    3    4   23                                                       
CONECT    4    3    6   24                                                  
CONECT    5    1   10   11                                                  
CONECT    6    4    7   13                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7   12   24                                                  
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   27                                                            
CONECT   17   27                                                            
CONECT   18   27                                                            
CONECT   19   28                                                            
CONECT   20   28                                                            
CONECT   21   29                                                            
CONECT   22   29                                                            
CONECT   23    3   28                                                       
CONECT   24    4    8                                                       
CONECT   25   27   29                                                       
CONECT   26   28   29                                                       
CONECT   27   16   17   18   25                                             
CONECT   28   19   20   23   26                                             
CONECT   29   21   22   25   26                                             
MASTER        0    0    0    0    0    0    0    0   29    0   60    0
END

Download
3D PDB for NP0333954 (Cytidine 5'-triphosphate)
Download
SMILES for NP0333954 (Cytidine 5'-triphosphate)
OC1C(O)C(OC1COP(O)(=O)OP(O)(=O)OP(O)(O)=O)N1C=CC(=N)N=C1O
Download
INCHI for NP0333954 (Cytidine 5'-triphosphate)
InChI=1/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)
Download
View in JSmol
Synonyms
ValueSource
Cytidine 5'-triphosphoric acidGenerator
Chemical FormulaC9H16N3O14P3
Average Mass483.1550 Da
Monoisotopic Mass482.98451 Da
IUPAC Name({[({[3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid
Traditional Name({[3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
OC1C(O)C(OC1COP(O)(=O)OP(O)(=O)OP(O)(O)=O)N1C=CC(=N)N=C1O
InChI Identifier
InChI=1/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)
InChI KeyPCDQPRRSZKQHHS-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3ChemAxon
pKa (Strongest Acidic)0.89ChemAxon
pKa (Strongest Basic)3.57ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area269.19 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity98.58 m³·mol⁻¹ChemAxon
Polarizability36.14 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Guo CJ, Zhang Z, Lu JL, Zhong J, Wu YF, Guo SY, Liu JL: Structural Basis of Bifunctional CTP/dCTP Synthase. J Mol Biol. 2024 Oct 15;436(20):168750. doi: 10.1016/j.jmb.2024.168750. Epub 2024  Aug 20. [PubMed:39173734  ] 
  2. Nakasuka F, Hirayama A, Makinoshima H, Yano S, Soga T, Tabata S: The role of cytidine 5'-triphosphate synthetase 1 in metabolic rewiring during epithelial-to-mesenchymal transition in non-small-cell lung cancer. FEBS Open Bio. 2024 Jul 19. doi: 10.1002/2211-5463.13860. [PubMed:39030877  ] 
  3. Liu Z, Sun M, Liu W, Feng F, Li X, Jin C, Zhang Y, Wang J: Deficiency of purinergic P2X4 receptor alleviates experimental autoimmune hepatitis in mice. Biochem Pharmacol. 2024 Mar;221:116033. doi: 10.1016/j.bcp.2024.116033. Epub 2024  Feb 1. [PubMed:38301964  ]