Human Metabolome Database: Showing metabocard for Zidovudine (HMDB0014638)

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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (5) Show 5 proteins XML

enzymes (5) Show 5 proteins

Record Information

Version

4.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:49 UTC

Update Date

2020-02-26 21:40:02 UTC

HMDB ID

HMDB0014638

Secondary Accession Numbers

HMDB14638

Metabolite Identification

Common Name

Zidovudine

Description

A dideoxynucleoside compound in which the 3'-hydroxy group on the sugar moiety has been replaced by an azido group. This modification prevents the formation of phosphodiester linkages which are needed for the completion of nucleic acid chains. The compound is a potent inhibitor of HIV replication, acting as a chain-terminator of viral DNA during reverse transcription. It improves immunologic function, partially reverses the HIV-induced neurological dysfunction, and improves certain other clinical abnormalities associated with AIDS. Its principal toxic effect is dose-dependent suppression of bone marrow, resulting in anemia and leukopenia. [PubChem]

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Azidothymidine	ChEBI
AZT	ChEBI
Retrovir	ChEBI
Zidovudin	ChEBI
Zidovudinum	ChEBI
3'-Azido-3'-deoxythymidine	Kegg
3'-Azido-2',3'-dideoxythymidine	HMDB
AZT antiviral	HMDB
BWA 509u	HMDB
AZT (antiviral)	HMDB
3' Azido 3' deoxythymidine	HMDB
Antiviral azt	HMDB
BW a509U	HMDB
3' Azido 2',3' dideoxythymidine	HMDB
AZT, antiviral	HMDB
BWA-509u	HMDB
BWA509u	HMDB

Chemical Formula

C₁₀H₁₃N₅O₄

Average Molecular Weight

267.2413

Monoisotopic Molecular Weight

267.096753929

IUPAC Name

1-[(2R,4S,5S)-4-azido-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

zidovudine

CAS Registry Number

30516-87-1

SMILES

CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO)O2)C(=O)NC1=O

InChI Identifier

InChI=1S/C10H13N5O4/c1-5-3-15(10(18)12-9(5)17)8-2-6(13-14-11)7(4-16)19-8/h3,6-8,16H,2,4H2,1H3,(H,12,17,18)/t6-,7+,8+/m0/s1

InChI Key

HBOMLICNUCNMMY-XLPZGREQSA-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
Pyrimidone
Hydroxypyrimidine
Hydropyrimidine
Pyrimidine
Tetrahydrofuran
Heteroaromatic compound
Azo imide
Azo compound
Oxacycle
Azacycle
Organoheterocyclic compound
Organic zwitterion
Alcohol
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

azide (CHEBI:10110 )
pyrimidine 2',3'-dideoxyribonucleoside (CHEBI:10110 )

Ontology

Physiological effect

Health effect:

Health condition:

Nervous system disorders:

Headache

Gastrointestinal disorders:

General disorders and administration site conditions:

Fatigue

Biofluid and excreta:

Cell and elements:

Extracellular

Subcellular:

Process

Naturally occurring process:

Biological process:

Biochemical pathway:

Zidovudine Action Pathway

Role

Industrial application:

Drug

Household products:

Antimicrobial agent:

Anti aids

Pharmaceutical industry:

Pharmaceutical

Enzyme inhibitor:

Reverse transcriptase inhibitor

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	106 - 112 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	16.3 g/L	Not Available
LogP	0.05	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	16.3 g/L	ALOGPS
logP	-0.1	ALOGPS
logP	-0.3	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	9.96	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	108.3 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	61.7 m³·mol⁻¹	ChemAxon
Polarizability	24.77 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-014i-9220000000-d55aacb79cb345dd1f0a	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0100-9631000000-1d566216a7cf9f0cc760	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-00di-0190000000-46ee7eb3034a9b20706d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-00di-0790000000-19916045eff2f2277d60	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0fk9-0900000000-836aff54cb90ce573db4	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-00di-0900000000-cb1ef888d872056bce56	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-00di-0900000000-97660ea43493fa2fa991	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-05fr-0900000000-407e81a32dbf5eb07134	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-004i-0900000000-743290b40f399a527da5	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-004i-0900000000-667b9ae1f4c499b8cef6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-004i-0900000000-c6bf89700e58ad9aff83	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-004i-1900000000-b644d0eec4449bae7675	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-01t9-2900000000-d794028d708aa5c5d04f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-03gi-5900000000-b2b0a6ddec7e2e91e8c4	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2090000000-d30081dd79d918431d63	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-4290000000-42d4b65040e25cf691f5	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9500000000-50cff13af2772ff9bd1e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0090000000-65bdc875b481997f35b0	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0090000000-cbe4e5e680eed587e220	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-007c-9200000000-9732b6de02e7378e613c	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Zidovudine 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 DB00495	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00495	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

DB00495

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

32555

KEGG Compound ID

C07210

BioCyc ID

CPD-15110

BiGG ID

Not Available

Wikipedia Link

Zidovudine

METLIN ID

Not Available

PubChem Compound

35370

PDB ID

Not Available

ChEBI ID

10110

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Mitsuya H, Yarchoan R, Broder S: Molecular targets for AIDS therapy. Science. 1990 Sep 28;249(4976):1533-44. [PubMed:1699273 ]
Mitsuya H, Weinhold KJ, Furman PA, St Clair MH, Lehrman SN, Gallo RC, Bolognesi D, Barry DW, Broder S: 3'-Azido-3'-deoxythymidine (BW A509U): an antiviral agent that inhibits the infectivity and cytopathic effect of human T-lymphotropic virus type III/lymphadenopathy-associated virus in vitro. Proc Natl Acad Sci U S A. 1985 Oct;82(20):7096-100. [PubMed:2413459 ]
Yarchoan R, Mitsuya H, Broder S: AIDS therapies. Sci Am. 1988 Oct;259(4):110-9. [PubMed:3072667 ]
De Clercq E: HIV resistance to reverse transcriptase inhibitors. Biochem Pharmacol. 1994 Jan 20;47(2):155-69. [PubMed:7508227 ]
Connor EM, Sperling RS, Gelber R, Kiselev P, Scott G, O'Sullivan MJ, VanDyke R, Bey M, Shearer W, Jacobson RL, et al.: Reduction of maternal-infant transmission of human immunodeficiency virus type 1 with zidovudine treatment. Pediatric AIDS Clinical Trials Group Protocol 076 Study Group. N Engl J Med. 1994 Nov 3;331(18):1173-80. [PubMed:7935654 ]
Court MH, Krishnaswamy S, Hao Q, Duan SX, Patten CJ, Von Moltke LL, Greenblatt DJ: Evaluation of 3'-azido-3'-deoxythymidine, morphine, and codeine as probe substrates for UDP-glucuronosyltransferase 2B7 (UGT2B7) in human liver microsomes: specificity and influence of the UGT2B7*2 polymorphism. Drug Metab Dispos. 2003 Sep;31(9):1125-33. [PubMed:12920168 ]

Enzymes

Enzyme Details

1. 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

2. 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

3. Cytochrome P450 2C19

General function:: Involved in monooxygenase activity
Specific function:: Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:: CYP2C19
Uniprot ID:: P33261
Molecular weight:: 55944.565

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 2C8

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. In the epoxidation of arachidonic acid it generates only 14,15- and 11,12-cis-epoxyeicosatrienoic acids. It is the principal enzyme responsible for the metabolism the anti-cancer drug paclitaxel (taxol).
Gene Name:: CYP2C8
Uniprot ID:: P10632
Molecular weight:: 55824.275

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 2A6

General function:: Involved in monooxygenase activity
Specific function:: Exhibits a high coumarin 7-hydroxylase activity. Can act in the hydroxylation of the anti-cancer drugs cyclophosphamide and ifosphamide. Competent in the metabolic activation of aflatoxin B1. Constitutes the major nicotine C-oxidase. Acts as a 1,4-cineole 2-exo-monooxygenase. Possesses low phenacetin O-deethylation activity.
Gene Name:: CYP2A6
Uniprot ID:: P11509
Molecular weight:: 56517.005

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 ]

Showing metabocard for Zidovudine (HMDB0014638)

Structure for HMDB0014638 (Zidovudine)

Enzymes

References

References

References

References

References