MiMeDB: Showing metabocard for cytidine 5'-diphosphoramidate (MMDBc0055843)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:08:33 UTC

Update Date

2022-08-12 20:09:28 UTC

Metabolite ID

MMDBc0055843

Metabolite Identification

Common Name

cytidine 5'-diphosphoramidate

Description

CDP-NH2 belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. Based on a literature review very few articles have been published on CDP-NH2.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222082D          

 29 30  0  0  1  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.2871    2.6392    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.9225    1.6607    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3086    2.0038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4143   -0.0143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9044    1.5549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9440    1.0253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1155    1.8322    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.1594    0.7703    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.5477    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -1.1299    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7132   -2.0662    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  1  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 12  5  1  0  0  0  0
 12  9  2  0  0  0  0
 13  2  1  0  0  0  0
  8 13  1  1  0  0  0
 13  9  1  0  0  0  0
  6 14  1  6  0  0  0
  7 15  1  6  0  0  0
 16  9  1  0  0  0  0
 21  3  1  0  0  0  0
 22  4  1  0  0  0  0
 22  8  1  0  0  0  0
 24 11  1  0  0  0  0
 24 17  1  0  0  0  0
 24 18  2  0  0  0  0
 24 23  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  2  0  0  0  0
 25 21  1  0  0  0  0
 25 23  1  0  0  0  0
  4 26  1  6  0  0  0
  6 27  1  1  0  0  0
  7 28  1  1  0  0  0
  8 29  1  6  0  0  0
M  CHG  2  16  -1  17  -1
M  END


  Mrv1652306172222082D          

 29 30  0  0  1  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.2871    2.6392    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.9225    1.6607    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3086    2.0038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4143   -0.0143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9044    1.5549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9440    1.0253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1155    1.8322    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.1594    0.7703    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.5477    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -1.1299    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7132   -2.0662    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  1  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 12  5  1  0  0  0  0
 12  9  2  0  0  0  0
 13  2  1  0  0  0  0
  8 13  1  1  0  0  0
 13  9  1  0  0  0  0
  6 14  1  6  0  0  0
  7 15  1  6  0  0  0
 16  9  1  0  0  0  0
 21  3  1  0  0  0  0
 22  4  1  0  0  0  0
 22  8  1  0  0  0  0
 24 11  1  0  0  0  0
 24 17  1  0  0  0  0
 24 18  2  0  0  0  0
 24 23  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  2  0  0  0  0
 25 21  1  0  0  0  0
 25 23  1  0  0  0  0
  4 26  1  6  0  0  0
  6 27  1  1  0  0  0
  7 28  1  1  0  0  0
  8 29  1  6  0  0  0
M  CHG  2  16  -1  17  -1
M  END
> <DATABASE_ID>
MMDBc0055843

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)[C@@]([H])(O)[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(N)([O-])=O)N1C=CC(=N)N=C1[O-]

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N4O10P2/c10-5-1-2-13(9(16)12-5)8-7(15)6(14)4(22-8)3-21-25(19,20)23-24(11,17)18/h1-2,4,6-8,14-15H,3H2,(H,19,20)(H2,10,12,16)(H3,11,17,18)/p-2/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
BSLSKFONEPFAKO-XVFCMESISA-L

> <FORMULA>
C9H14N4O10P2

> <MOLECULAR_WEIGHT>
400.178

> <EXACT_MASS>
400.019613823

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
31.348974536384034

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_LOGP>
-4.115793193199554

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.151538137356754

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.4539910953147235

> <JCHEM_PKA_STRONGEST_BASIC>
2.5403209173149772

> <JCHEM_POLAR_SURFACE_AREA>
234.10999999999996

> <JCHEM_REFRACTIVITY>
98.66709999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       3.182  -6.383   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.087  -5.138   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.846  -0.544   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.650  -6.222   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.929  -3.570   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.745  -7.468   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0      11.736   4.927   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       1.024  -4.816   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       3.460  -3.731   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.302  -2.163   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0      12.922   3.100   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       9.909   3.740   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      10.107  -0.027   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.155   2.903   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.166   0.962   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       5.906  -2.485   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      11.095   1.914   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0      11.416   3.420   0.000  0.00  0.00           P+0
HETATM   25  P   UNK     0       9.631   1.438   0.000  0.00  0.00           P+0
HETATM   26  H   UNK     0       6.622   0.501   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.763   0.584   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       2.801  -2.109   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0       5.065  -3.857   0.000  0.00  0.00           H+0
CONECT    1    2    5                                                       
CONECT    2    1   13                                                       
CONECT    3    4   21                                                       
CONECT    4    3    6   22   26                                             
CONECT    5    1   10   12                                                  
CONECT    6    4    7   14   27                                             
CONECT    7    6    8   15   28                                             
CONECT    8    7   13   22   29                                             
CONECT    9   12   13   16                                                  
CONECT   10    5                                                            
CONECT   11   24                                                            
CONECT   12    5    9                                                       
CONECT   13    2    8    9                                                  
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16    9                                                            
CONECT   17   24                                                            
CONECT   18   24                                                            
CONECT   19   25                                                            
CONECT   20   25                                                            
CONECT   21    3   25                                                       
CONECT   22    4    8                                                       
CONECT   23   24   25                                                       
CONECT   24   11   17   18   23                                             
CONECT   25   19   20   21   23                                             
CONECT   26    4                                                            
CONECT   27    6                                                            
CONECT   28    7                                                            
CONECT   29    8                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   60    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₄N₄O₁₀P₂

Average Mass

400.178

Monoisotopic Mass

400.019613823

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)[C@@]([H])(O)[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(N)([O-])=O)N1C=CC(=N)N=C1[O-]

InChI Identifier

InChI=1S/C9H16N4O10P2/c10-5-1-2-13(9(16)12-5)8-7(15)6(14)4(22-8)3-21-25(19,20)23-24(11,17)18/h1-2,4,6-8,14-15H,3H2,(H,19,20)(H2,10,12,16)(H3,11,17,18)/p-2/t4-,6-,7-,8-/m1/s1

InChI Key

BSLSKFONEPFAKO-XVFCMESISA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Monoalkyl phosphate
Organic phosphoric acid amide
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Alcohol
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.1	ChemAxon
pKa (Strongest Acidic)	0.45	ChemAxon
pKa (Strongest Basic)	2.54	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	234.11 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	98.67 m³·mol⁻¹	ChemAxon
Polarizability	31.35 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

134716619

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for cytidine 5'-diphosphoramidate (MMDBc0055843)

MOL for #<Metabolite:0x00007fecaf11fc80>

3D MOL for #<Metabolite:0x00007fecaf11fc80>

3D SDF for #<Metabolite:0x00007fecaf11fc80>

3D-SDF for #<Metabolite:0x00007fecaf11fc80>

PDB for #<Metabolite:0x00007fecaf11fc80>

3D PDB for #<Metabolite:0x00007fecaf11fc80>

SMILES for #<Metabolite:0x00007fecaf11fc80>

INCHI for #<Metabolite:0x00007fecaf11fc80>

Structure for #<Metabolite:0x00007fecaf11fc80>

3D Structure for #<Metabolite:0x00007fecaf11fc80>