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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (7)transporters (2) Show 9 proteins XML

enzymes (7)transporters (2) Show 9 proteins

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:51 UTC

Update Date

2022-03-07 02:51:51 UTC

HMDB ID

HMDB0015078

Secondary Accession Numbers

HMDB15078

Metabolite Identification

Common Name

Zalcitabine

Description

A dideoxynucleoside compound in which the 3'-hydroxyl group on the sugar moiety has been replaced by a hydrogen. This modification prevents the formation of 5' to 3' phosphodiester linkages, which are needed for the elongation of DNA chains, thus resulting in the termination of viral DNA growth. The compound is a potent inhibitor of HIV replication at low concentrations, acting as a chain-terminator of viral DNA by binding to reverse transcriptase. Its principal toxic side effect is axonal degeneration resulting in peripheral neuropathy. [PubChem]

Structure

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

943
  Mrv0541 02231215072D          

 15 16  0  0  1  0            999 V2000
    3.7465   -0.7106    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6409   -2.9164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.5994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.5994    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    1.8369    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    3.0744    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.2256    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4115   -0.7106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6665   -1.4952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4916   -1.4952    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9764   -2.1627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    1.0119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    1.0119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    1.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    2.2494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1 10  1  0  0  0  0
  2 11  1  0  0  0  0
  3 13  2  0  0  0  0
  7  4  1  6  0  0  0
  4 12  1  0  0  0  0
  4 13  1  0  0  0  0
  5 13  1  0  0  0  0
  5 15  2  0  0  0  0
  6 15  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 12 14  2  0  0  0  0
 14 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0015078

> <DATABASE_NAME>
hmdb

> <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    HMDB0015078
HETATM    1  N1  UNL     1       5.039  -0.036   1.104  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.690   0.042   0.705  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.350   0.221  -0.635  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.013   0.289  -0.957  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.026   0.191  -0.046  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.329   0.279  -0.516  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.826  -1.027  -1.109  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.333  -0.742  -1.158  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.462   0.416  -0.219  1.00  0.00           C  
HETATM   10  C8  UNL     1      -3.629   0.252   0.737  1.00  0.00           C  
HETATM   11  O1  UNL     1      -3.750   1.316   1.600  1.00  0.00           O  
HETATM   12  O2  UNL     1      -1.254   0.524   0.467  1.00  0.00           O  
HETATM   13  C9  UNL     1       1.379   0.020   1.227  1.00  0.00           C  
HETATM   14  O3  UNL     1       0.433  -0.070   2.072  1.00  0.00           O  
HETATM   15  N3  UNL     1       2.662  -0.050   1.575  1.00  0.00           N  
HETATM   16  H1  UNL     1       5.374   0.522   1.902  1.00  0.00           H  
HETATM   17  H2  UNL     1       5.689  -0.653   0.596  1.00  0.00           H  
HETATM   18  H3  UNL     1       4.154   0.297  -1.345  1.00  0.00           H  
HETATM   19  H4  UNL     1       1.761   0.431  -2.019  1.00  0.00           H  
HETATM   20  H5  UNL     1      -0.449   1.055  -1.306  1.00  0.00           H  
HETATM   21  H6  UNL     1      -0.420  -1.200  -2.119  1.00  0.00           H  
HETATM   22  H7  UNL     1      -0.685  -1.875  -0.416  1.00  0.00           H  
HETATM   23  H8  UNL     1      -2.913  -1.623  -0.863  1.00  0.00           H  
HETATM   24  H9  UNL     1      -2.537  -0.420  -2.208  1.00  0.00           H  
HETATM   25  H10 UNL     1      -2.589   1.347  -0.808  1.00  0.00           H  
HETATM   26  H11 UNL     1      -3.611  -0.740   1.232  1.00  0.00           H  
HETATM   27  H12 UNL     1      -4.550   0.248   0.095  1.00  0.00           H  
HETATM   28  H13 UNL     1      -4.231   0.989   2.414  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 View NMR Assignments View Stereo Labels

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
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 Molecular Weight

211.2178

Monoisotopic Molecular Weight

211.095691297

IUPAC Name

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

Traditional Name

zalcitabine

CAS Registry Number

7481-89-2

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

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

Substituents

Pyrimidine 2',3'-dideoxyribonucleoside
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Alcohol
Amine
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2',3'-dideoxyribonucleoside (CHEBI:10101 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Biofluid or Excreta

Excreta

Urine (PMID: 21059682)

Non-excretory biofluid

Blood (PMID: 21059682)

Process

Naturally occurring process

Biological process

Biochemical pathway

Drug action pathway

Zalcitabine Action Pathway (PathBank: SMP0000746)

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	210 - 214 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	7.05 g/L	Not Available
LogP	-1.3	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	7.05 g/L	ALOGPS
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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	147.58	31661259
DarkChem	[M-H]-	145.569	31661259
DeepCCS	[M+H]+	146.918	30932474
DeepCCS	[M-H]-	144.522	30932474
DeepCCS	[M-2H]-	177.617	30932474
DeepCCS	[M+Na]+	152.909	30932474
AllCCS	[M+H]+	147.9	32859911
AllCCS	[M+H-H2O]+	143.8	32859911
AllCCS	[M+NH4]+	151.6	32859911
AllCCS	[M+Na]+	152.7	32859911
AllCCS	[M-H]-	148.0	32859911
AllCCS	[M+Na-2H]-	148.2	32859911
AllCCS	[M+HCOO]-	148.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Zalcitabine	NC1=NC(=O)N(C=C1)[C@H]1CC[C@@H](CO)O1	3389.1	Standard polar	33892256
Zalcitabine	NC1=NC(=O)N(C=C1)[C@H]1CC[C@@H](CO)O1	2186.3	Standard non polar	33892256
Zalcitabine	NC1=NC(=O)N(C=C1)[C@H]1CC[C@@H](CO)O1	2357.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Zalcitabine,1TMS,isomer #1	C[Si](C)(C)OC[C@@H]1CC[C@H](N2C=CC(N)=NC2=O)O1	2141.1	Semi standard non polar	33892256
Zalcitabine,1TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N([C@H]2CC[C@@H](CO)O2)C=C1	2226.8	Semi standard non polar	33892256
Zalcitabine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2CC[C@@H](CO[Si](C)(C)C)O2)C=C1	2203.7	Semi standard non polar	33892256
Zalcitabine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2CC[C@@H](CO[Si](C)(C)C)O2)C=C1	2293.5	Standard non polar	33892256
Zalcitabine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2CC[C@@H](CO[Si](C)(C)C)O2)C=C1	3003.8	Standard polar	33892256
Zalcitabine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N([C@H]2CC[C@@H](CO)O2)C=C1)[Si](C)(C)C	2190.5	Semi standard non polar	33892256
Zalcitabine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N([C@H]2CC[C@@H](CO)O2)C=C1)[Si](C)(C)C	2350.5	Standard non polar	33892256
Zalcitabine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N([C@H]2CC[C@@H](CO)O2)C=C1)[Si](C)(C)C	3026.3	Standard polar	33892256
Zalcitabine,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1CC[C@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O1	2176.4	Semi standard non polar	33892256
Zalcitabine,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1CC[C@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O1	2377.7	Standard non polar	33892256
Zalcitabine,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1CC[C@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O1	2666.1	Standard polar	33892256
Zalcitabine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1CC[C@H](N2C=CC(N)=NC2=O)O1	2403.1	Semi standard non polar	33892256
Zalcitabine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2CC[C@@H](CO)O2)C=C1	2473.4	Semi standard non polar	33892256
Zalcitabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2CC[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1	2658.7	Semi standard non polar	33892256
Zalcitabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2CC[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1	2724.4	Standard non polar	33892256
Zalcitabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2CC[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1	3091.9	Standard polar	33892256
Zalcitabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@H]2CC[C@@H](CO)O2)C=C1)[Si](C)(C)C(C)(C)C	2615.6	Semi standard non polar	33892256
Zalcitabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@H]2CC[C@@H](CO)O2)C=C1)[Si](C)(C)C(C)(C)C	2797.7	Standard non polar	33892256
Zalcitabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@H]2CC[C@@H](CO)O2)C=C1)[Si](C)(C)C(C)(C)C	3060.7	Standard polar	33892256
Zalcitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1CC[C@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O1	2818.3	Semi standard non polar	33892256
Zalcitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1CC[C@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O1	3011.3	Standard non polar	33892256
Zalcitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1CC[C@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O1	2910.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Zalcitabine GC-MS (Non-derivatized) - 70eV, Positive	splash10-005c-9600000000-2b4de4867a39d5e3055b	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Zalcitabine GC-MS (1 TMS) - 70eV, Positive	splash10-00b9-9800000000-add2e4ce43f76aa31304	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Zalcitabine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , negative-QTOF	splash10-03di-0190000000-5d3365f648d5f5675ab9	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , negative-QTOF	splash10-066r-2900000000-843d28df71eab94652c3	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , negative-QTOF	splash10-0a4l-7900000000-628c9e8f6a131581a8d4	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , negative-QTOF	splash10-0006-9200000000-60a00651a71121843a19	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , negative-QTOF	splash10-0006-9000000000-237a0c1094225974a6e8	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , positive-QTOF	splash10-03di-0910000000-95a2a7845a54a61d7c15	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , positive-QTOF	splash10-03di-0900000000-345deba429b644c7b4f5	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , positive-QTOF	splash10-03di-0900000000-6aaba2f2eeb001628ab2	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , positive-QTOF	splash10-03di-5900000000-03b881f85c17ccbe5295	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-QQ , positive-QTOF	splash10-01ot-9300000000-2896ce7406bb834c001a	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine LC-ESI-IT , positive-QTOF	splash10-03di-0900000000-056961b8bc4067346530	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Zalcitabine 35V, Positive-QTOF	splash10-03di-1900000000-1054737ea962191f8ea3	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 10V, Negative-QTOF	splash10-03di-1980000000-983fc19dcf0d0b85cef4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 20V, Negative-QTOF	splash10-014i-2900000000-0612e4906539771bd61a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 40V, Negative-QTOF	splash10-0006-9300000000-b05fd7cbb391f9d8d755	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 10V, Negative-QTOF	splash10-03di-0490000000-57082a1867cdc2c9822a	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 20V, Negative-QTOF	splash10-01ox-9600000000-f474e998724df983de8c	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 40V, Negative-QTOF	splash10-0006-9300000000-20ef263f8c644fd3e58e	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 10V, Positive-QTOF	splash10-03di-0900000000-eaacef912c49eac35506	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 20V, Positive-QTOF	splash10-03di-4900000000-0712eb98271c7def7fa6	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 40V, Positive-QTOF	splash10-0292-9300000000-b5ae4987aabc3d08e09b	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 10V, Positive-QTOF	splash10-03di-0900000000-fa8c6be751e9c08c099b	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 20V, Positive-QTOF	splash10-03di-3900000000-acfad49c533143abebc1	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zalcitabine 40V, Positive-QTOF	splash10-014i-9100000000-9b080034478e10638d8e	2021-10-11	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Zalcitabine Action Pathway		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00943	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00943	21059682	details

Abnormal Concentrations

Not Available

Predicted Concentrations

Biospecimen	Value	Original age	Original sex	Original condition	Comments
Blood	0.000 uM	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities
Blood	0.000 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00943

Phenol Explorer Compound ID

Not Available

FooDB 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

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Devineni D, Gallo JM: Zalcitabine. Clinical pharmacokinetics and efficacy. Clin Pharmacokinet. 1995 May;28(5):351-60. [PubMed:7614775 ]
Shelton MJ, O'Donnell AM, Morse GD: Zalcitabine. Ann Pharmacother. 1993 Apr;27(4):480-9. [PubMed:8097417 ]

Enzymes

Enzyme Details

1. Deoxycytidine kinase

General function:: Involved in ATP binding
Specific function:: Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:: DCK
Uniprot ID:: P27707
Molecular weight:: 30518.315

References

Rossi L, Serafini S, Schiavano GF, Casabianca A, Vallanti G, Chiarantini L, Magnani M: Metabolism, mitochondrial uptake and toxicity of 2', 3'-dideoxycytidine. Biochem J. 1999 Dec 15;344 Pt 3:915-20. [PubMed:10585881 ]
Kitos TE, Tyrrell DL: Intracellular metabolism of 2',3'-dideoxynucleosides in duck hepatocyte primary cultures. Biochem Pharmacol. 1995 May 11;49(9):1291-302. [PubMed:7763311 ]

Enzyme Details

2. Cytochrome P450 3A4

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:: CYP3A4
Uniprot ID:: P08684
Molecular weight:: 57255.585

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

3. Cytochrome P450 2C9

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.
Gene Name:: CYP2C9
Uniprot ID:: P11712
Molecular weight:: 55627.365

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

4. Cytochrome P450 3A43

General function:: Involved in monooxygenase activity
Specific function:: Exhibits low testosterone 6-beta-hydroxylase activity.
Gene Name:: CYP3A43
Uniprot ID:: Q9HB55
Molecular weight:: 57756.285

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

5. Cytochrome P450 2D6

General function:: Involved in monooxygenase activity
Specific function:: Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.
Gene Name:: CYP2D6
Uniprot ID:: P10635
Molecular weight:: 55768.94

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

6. Cytochrome P450 3A5

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:: CYP3A5
Uniprot ID:: P20815
Molecular weight:: 57108.065

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

7. Cytochrome P450 3A7

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:: CYP3A7
Uniprot ID:: P24462
Molecular weight:: 57525.03

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Transporters

Enzyme Details

1. Solute carrier family 22 member 6

General function:: Involved in ion transmembrane transporter activity
Specific function:: Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of 2,3-dimercapto-1-propanesulfonic acid (DMPS). Mediates the sodium-independent uptake of p- aminohippurate (PAH), ochratoxin (OTA), acyclovir (ACV), 3'-azido- 3-'deoxythymidine (AZT), cimetidine (CMD), 2,4-dichloro- phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS) and 3-carboxy-4-methyl-5-propyl-2- furanpropionate (CMPF), cidofovir, adefovir, 9-(2- phosphonylmethoxyethyl) guanine (PMEG), 9-(2- phosphonylmethoxyethyl) diaminopurine (PMEDAP) and edaravone sulfate. PAH uptake is inhibited by p- chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), sulindac, diclofenac, carprofen, glutarate and okadaic acid. PAH uptake is inhibited by benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, furosemide, indomethacin, bumetamide, losartan, probenecid, phenol red, urate, and alpha-ketoglutarate
Gene Name:: SLC22A6
Uniprot ID:: Q4U2R8
Molecular weight:: 61815.8

References

Wada S, Tsuda M, Sekine T, Cha SH, Kimura M, Kanai Y, Endou H: Rat multispecific organic anion transporter 1 (rOAT1) transports zidovudine, acyclovir, and other antiviral nucleoside analogs. J Pharmacol Exp Ther. 2000 Sep;294(3):844-9. [PubMed:10945832 ]

Enzyme Details

2. Solute carrier family 22 member 7

General function:: Involved in transmembrane transport
Specific function:: Mediates sodium-independent multispecific organic anion transport. Transport of prostaglandin E2, prostaglandin F2, tetracycline, bumetanide, estrone sulfate, glutarate, dehydroepiandrosterone sulfate, allopurinol, 5-fluorouracil, paclitaxel, L-ascorbic acid, salicylate, ethotrexate, and alpha- ketoglutarate
Gene Name:: SLC22A7
Uniprot ID:: Q9Y694
Molecular weight:: 60025.0

References

Morita N, Kusuhara H, Sekine T, Endou H, Sugiyama Y: Functional characterization of rat organic anion transporter 2 in LLC-PK1 cells. J Pharmacol Exp Ther. 2001 Sep;298(3):1179-84. [PubMed:11504818 ]

Showing metabocard for Zalcitabine (HMDB0015078)

MOL for HMDB0015078 (Zalcitabine)

3D MOL for HMDB0015078 (Zalcitabine)

3D SDF for HMDB0015078 (Zalcitabine)

3D-SDF for HMDB0015078 (Zalcitabine)

PDB for HMDB0015078 (Zalcitabine)

3D PDB for HMDB0015078 (Zalcitabine)

SMILES for HMDB0015078 (Zalcitabine)

INCHI for HMDB0015078 (Zalcitabine)

Structure for HMDB0015078 (Zalcitabine)

3D Structure for HMDB0015078 (Zalcitabine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

References

References

References

References

References

References

References

Transporters

References

References