NP-MRD: Showing NP-Card for 2,3-Dideoxycytidine (NP0002865)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2020-11-23 19:42:20 UTC

Updated at

2021-08-12 19:52:22 UTC

NP-MRD ID

NP0002865

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,3-Dideoxycytidine

Provided By

BMRB

Description

Zalcitabine, also known as DDC or hivid, belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3. Zalcitabine is a drug which is used for the treatment of human immunovirus (hiv) infections in conjunction with other antivirals. In humans, zalcitabine is involved in the zalcitabine action pathway. Zalcitabine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Zalcitabine is formally rated as a possible carcinogen (by IARC 2B) and is also a potentially toxic compound. It was first documented in 1993 (PMID: 8097417). Based on a literature review a significant number of articles have been published on Zalcitabine (PMID: 17984079) (PMID: 7614775) (PMID: 11905988) (PMID: 7727578).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


     RDKit          2D

 28 29  0  0  0  0  0  0  0  0999 V2000
   -4.9944   -1.2092    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6149   -0.6201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4353    0.8691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0558    1.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8559    0.5579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5236    1.1469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7505    2.0099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9504    1.1097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4650   -0.3096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2854   -1.7988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1058   -3.2880    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9652   -0.2866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0355   -0.9313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0625   -1.8670    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4151   -1.5203    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1741   -2.6984    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1943   -0.3090    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6351    1.7692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8761    2.9473    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2064    2.4573    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7640    3.1399    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7712    3.1091    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7202    2.3971    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3112    0.4787    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9273   -0.6439    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7746   -1.9784    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9354   -1.8017    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3056   -4.1882    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  5 13  1  0
 13 14  2  0
 13 15  1  0
 15  2  2  0
 12  6  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  6
  7 21  1  6
  7 22  1  0
  8 23  1  1
  8 24  1  0
  9 25  1  6
 10 26  1  6
 10 27  1  0
 11 28  1  0
M  END
> <DATABASE_ID>
NP0002865

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC(=O)N(C=C1)[C@H]1CC[C@@H](CO)O1

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N3O3/c10-7-3-4-12(9(14)11-7)8-2-1-6(5-13)15-8/h3-4,6,8,13H,1-2,5H2,(H2,10,11,14)/t6-,8+/m0/s1

> <INCHI_KEY>
WREGKURFCTUGRC-POYBYMJQSA-N

> <FORMULA>
C9H13N3O3

> <MOLECULAR_WEIGHT>
211.2178

> <EXACT_MASS>
211.095691297

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
20.858874948562367

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2R,5S)-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.29

> <JCHEM_LOGP>
-1.1882264563333331

> <ALOGPS_LOGS>
-1.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.673301594378366

> <JCHEM_PKA_STRONGEST_BASIC>
0.1760531801028753

> <JCHEM_POLAR_SURFACE_AREA>
88.15

> <JCHEM_REFRACTIVITY>
52.24020000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.05e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
zalcitabine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 943                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       6.993  -1.326   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       6.796  -5.444   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       3.080   1.119   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       5.748   1.119   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       4.414   3.429   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       5.748   5.739   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       5.748  -0.421   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.501  -1.326   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.977  -2.791   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.518  -2.791   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.423  -4.037   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.081   1.889   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.414   1.889   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.081   3.429   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.748   4.199   0.000  0.00  0.00           C+0
CONECT    1    7   10                                                       
CONECT    2   11                                                            
CONECT    3   13                                                            
CONECT    4    7   12   13                                                  
CONECT    5   13   15                                                       
CONECT    6   15                                                            
CONECT    7    1    4    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    1    9   11                                                  
CONECT   11    2   10                                                       
CONECT   12    4   14                                                       
CONECT   13    3    4    5                                                  
CONECT   14   12   15                                                       
CONECT   15    5    6   14                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

COMPND    NP0002865
HETATM    1  N1  UNL     1      -5.003   0.835  -0.959  1.00  0.00           N  
HETATM    2  C1  UNL     1      -3.655   0.441  -0.662  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.117   0.640   0.592  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.823   0.261   0.872  1.00  0.00           C  
HETATM    5  N2  UNL     1      -1.053  -0.317  -0.085  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.277  -0.686   0.268  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.144  -1.205  -0.815  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.489  -1.253  -0.066  1.00  0.00           C  
HETATM    9  C7  UNL     1       2.301  -0.128   0.925  1.00  0.00           C  
HETATM   10  C8  UNL     1       3.397   0.880   0.673  1.00  0.00           C  
HETATM   11  O1  UNL     1       3.323   1.982   1.504  1.00  0.00           O  
HETATM   12  O2  UNL     1       1.042   0.385   0.744  1.00  0.00           O  
HETATM   13  C9  UNL     1      -1.598  -0.500  -1.295  1.00  0.00           C  
HETATM   14  O3  UNL     1      -0.866  -1.040  -2.175  1.00  0.00           O  
HETATM   15  N3  UNL     1      -2.869  -0.128  -1.572  1.00  0.00           N  
HETATM   16  H1  UNL     1      -5.198   1.347  -1.846  1.00  0.00           H  
HETATM   17  H2  UNL     1      -5.718   0.584  -0.267  1.00  0.00           H  
HETATM   18  H3  UNL     1      -3.749   1.105   1.347  1.00  0.00           H  
HETATM   19  H4  UNL     1      -1.436   0.439   1.885  1.00  0.00           H  
HETATM   20  H5  UNL     1       0.244  -1.429   1.083  1.00  0.00           H  
HETATM   21  H6  UNL     1       0.882  -2.216  -1.185  1.00  0.00           H  
HETATM   22  H7  UNL     1       1.330  -0.473  -1.635  1.00  0.00           H  
HETATM   23  H8  UNL     1       2.600  -2.229   0.453  1.00  0.00           H  
HETATM   24  H9  UNL     1       3.317  -1.089  -0.766  1.00  0.00           H  
HETATM   25  H10 UNL     1       2.379  -0.512   1.983  1.00  0.00           H  
HETATM   26  H11 UNL     1       3.338   1.191  -0.379  1.00  0.00           H  
HETATM   27  H12 UNL     1       4.371   0.347   0.792  1.00  0.00           H  
HETATM   28  H13 UNL     1       3.650   2.765   0.972  1.00  0.00           H  
CONECT    1    2   16   17
CONECT    2    3   15   15
CONECT    3    4    4   18
CONECT    4    5   19
CONECT    5    6   13
CONECT    6    7   12   20
CONECT    7    8   21   22
CONECT    8    9   23   24
CONECT    9   10   12   25
CONECT   10   11   26   27
CONECT   11   28
CONECT   13   14   14   15
END

View in JSmol

Synonyms

Value	Source
2',3'-Dideoxycytidine	ChEBI
4-Amino-1-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2(1H)-one	ChEBI
DDC	ChEBI
DDCYD	ChEBI
Dideoxycytidine	ChEBI
Hivid	Kegg
ABBR DDC	Kegg
HIVID roche	HMDB
2',3' Dideoxycytidine	HMDB
Hoffman-la roche brand OF zalcitabine	HMDB
Roche brand OF zalcitabine	HMDB
DDC (Antiviral)	HMDB

Chemical Formula

C₉H₁₃N₃O₃

Average Mass

211.2178 Da

Monoisotopic Mass

211.09569 Da

IUPAC Name

4-amino-1-[(2R,5S)-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

zalcitabine

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)[C@H]1CC[C@@H](CO)O1

InChI Identifier

InChI=1S/C9H13N3O3/c10-7-3-4-12(9(14)11-7)8-2-1-6(5-13)15-8/h3-4,6,8,13H,1-2,5H2,(H2,10,11,14)/t6-,8+/m0/s1

InChI Key

WREGKURFCTUGRC-POYBYMJQSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2',3'-dideoxyribonucleosides

Direct Parent

Pyrimidine 2',3'-dideoxyribonucleosides

Alternative Parents

Not Available

Substituents

Not Available

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	-1.3	ALOGPS
logP	-1.2	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	14.67	ChemAxon
pKa (Strongest Basic)	0.18	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	88.15 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.24 m³·mol⁻¹	ChemAxon
Polarizability	20.86 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0015078

DrugBank ID

DB00943

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

22498

KEGG Compound ID

C07207

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Zalcitabine

METLIN ID

Not Available

PubChem Compound

24066

PDB ID

Not Available

ChEBI ID

10101

Good Scents ID

Not Available

References

General References

Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
Devineni D, Gallo JM: Zalcitabine. Clinical pharmacokinetics and efficacy. Clin Pharmacokinet. 1995 May;28(5):351-60. doi: 10.2165/00003088-199528050-00002. [PubMed:7614775 ]
Shelton MJ, O'Donnell AM, Morse GD: Zalcitabine. Ann Pharmacother. 1993 Apr;27(4):480-9. doi: 10.1177/106002809302700416. [PubMed:8097417 ]
Gibbs JE, Thomas SA: The distribution of the anti-HIV drug, 2'3'-dideoxycytidine (ddC), across the blood-brain and blood-cerebrospinal fluid barriers and the influence of organic anion transport inhibitors. J Neurochem. 2002 Feb;80(3):392-404. doi: 10.1046/j.0022-3042.2001.00711.x. [PubMed:11905988 ]
Torres RA, Barr MR, McIntyre KI, Thornton JR, Shay WM, Feldman RD, George NJ, Britton DJ: A comparison of zidovudine, didanosine, zalcitabine and no antiretroviral therapy in patients with advanced HIV disease. Int J STD AIDS. 1995 Jan-Feb;6(1):19-26. doi: 10.1177/095646249500600105. [PubMed:7727578 ]

Showing NP-Card for 2,3-Dideoxycytidine (NP0002865)

MOL for NP0002865 (2,3-Dideoxycytidine)

3D MOL for NP0002865 (2,3-Dideoxycytidine)

3D SDF for NP0002865 (2,3-Dideoxycytidine)

3D-SDF for NP0002865 (2,3-Dideoxycytidine)

PDB for NP0002865 (2,3-Dideoxycytidine)

3D PDB for NP0002865 (2,3-Dideoxycytidine)

SMILES for NP0002865 (2,3-Dideoxycytidine)

INCHI for NP0002865 (2,3-Dideoxycytidine)

Structure for NP0002865 (2,3-Dideoxycytidine)

3D Structure for NP0002865 (2,3-Dideoxycytidine)