NP-MRD: Showing NP-Card for 1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol (NP0328275)

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Record Information

Version

2.0

Created at

2022-09-12 11:36:06 UTC

Updated at

2022-09-12 11:36:06 UTC

NP-MRD ID

NP0328275

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol

Description

Lamivudine, also known as 3TC or epivir, belongs to the class of organic compounds known as 3'-thia pyrimidine nucleosides. These are nucleoside analogues with a structure that consists of a pyrimidine base, which is N-substituted at the 1-position with a 3'-thia derivative (1,3-oxazolidine) of the ribose moiety that is characteristic of nucleosides. Lamivudine is a drug which is used for the treatment of hiv infection and chronic hepatitis b (hbv). Lamivudine is an extremely weak basic (essentially neutral) compound (based on its pKa). Within humans, lamivudine participates in a number of enzymatic reactions. In particular, lamivudine and uridine triphosphate can be biosynthesized from lamivudine-monophosphate and uridine 5'-diphosphate through the action of the enzyme 5'(3')-deoxyribonucleotidase, cytosolic type. In addition, lamivudine can be converted into lamivudine sulfoxide; which is mediated by the enzyme sulfotransferase 1A1. In humans, lamivudine is involved in lamivudine metabolism pathway. 1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol was first documented in 2002 (PMID: 12135009). A monothioacetal that consists of cytosine having a (2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl moiety attached at position 1 (PMID: 17310820) (PMID: 19783232) (PMID: 21465499) (PMID: 21721935).

Structure

MOL 3D MOL SDF PDB SMILES InChI

709
  Mrv0541 02231214572D          

 15 16  0  0  1  0            999 V2000
    2.6665   -1.4952    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    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  2  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
    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  9  1  0  0  0  0
  1 10  1  0  0  0  0
  2  8  1  0  0  0  0
  2 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 13  2  0  0  0  0
  8  5  1  1  0  0  0
  5 12  1  0  0  0  0
  5 13  1  0  0  0  0
  6 13  1  0  0  0  0
  6 15  2  0  0  0  0
  7 15  1  0  0  0  0
  8  9  1  0  0  0  0
 10 11  1  1  0  0  0
 12 14  2  0  0  0  0
 14 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0328275

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H11N3O3S/c9-5-1-2-11(8(13)10-5)6-4-15-7(3-12)14-6/h1-2,6-7,12H,3-4H2,(H2,9,10,13)/t6-,7+/m0/s1

> <INCHI_KEY>
JTEGQNOMFQHVDC-NKWVEPMBSA-N

> <FORMULA>
C8H11N3O3S

> <MOLECULAR_WEIGHT>
229.256

> <EXACT_MASS>
229.052111923

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
21.69986366490535

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.29

> <JCHEM_LOGP>
-1.0951075880000003

> <ALOGPS_LOGS>
-1.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.294605913828615

> <JCHEM_PKA_STRONGEST_BASIC>
-0.16058074296490987

> <JCHEM_POLAR_SURFACE_AREA>
88.15

> <JCHEM_REFRACTIVITY>
55.1645

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.76e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lamivudine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 709                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  S   UNK     0       4.977  -2.791   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0       6.993  -1.326   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       6.796  -5.444   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.080   1.119   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       5.748   1.119   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       4.414   3.429   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       5.748   5.739   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       5.748  -0.421   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.501  -1.326   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    9   10                                                       
CONECT    2    8   10                                                       
CONECT    3   11                                                            
CONECT    4   13                                                            
CONECT    5    8   12   13                                                  
CONECT    6   13   15                                                       
CONECT    7   15                                                            
CONECT    8    2    5    9                                                  
CONECT    9    1    8                                                       
CONECT   10    1    2   11                                                  
CONECT   11    3   10                                                       
CONECT   12    5   14                                                       
CONECT   13    4    5    6                                                  
CONECT   14   12   15                                                       
CONECT   15    6    7   14                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Value	Source
(-)-1-((2R,5S)-2-(Hydroxymethyl)-1,3-oxathiolan-5-yl)cytosine	ChEBI
(-)-2'-Deoxy-3'-thiacytidine	ChEBI
2',3'-Dideoxy-3'-thiacytidine	ChEBI
3'-Thia-2',3'-dideoxycytidine	ChEBI
3TC	ChEBI
beta-L-2',3'-Dideoxy-3'-thiacytidine	ChEBI
beta-L-3'-Thia-2',3'-dideoxycytidine	ChEBI
Epivir	ChEBI
b-L-2',3'-Dideoxy-3'-thiacytidine	Generator
Β-L-2',3'-dideoxy-3'-thiacytidine	Generator
b-L-3'-Thia-2',3'-dideoxycytidine	Generator
Β-L-3'-thia-2',3'-dideoxycytidine	Generator
2',3' Dideoxy 3' thiacytidine	HMDB
BCH 189	HMDB
BCH-189	HMDB
Lamivudine, (2S-cis)-isomer	HMDB

Chemical Formula

C₈H₁₁N₃O₃S

Average Mass

229.2560 Da

Monoisotopic Mass

229.05211 Da

IUPAC Name

4-amino-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

lamivudine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C8H11N3O3S/c9-5-1-2-11(8(13)10-5)6-4-15-7(3-12)14-6/h1-2,6-7,12H,3-4H2,(H2,9,10,13)/t6-,7+/m0/s1

InChI Key

JTEGQNOMFQHVDC-NKWVEPMBSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3'-thia pyrimidine nucleosides. These are nucleoside analogues with a structure that consists of a pyrimidine base, which is N-substituted at the 1-position with a 3'-thia derivative (1,3-oxazolidine) of the ribose moiety that is characteristic of nucleosides.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Nucleoside and nucleotide analogues

Sub Class

3'-thia pyrimidine nucleosides

Direct Parent

3'-thia pyrimidine nucleosides

Alternative Parents

Substituents

3'-thia pyrimidine nucleoside
Hydroxypyrimidine
Hydropyrimidine
Pyrimidine
Monothioacetal
Oxathiolane
Heteroaromatic compound
Azacycle
Organoheterocyclic compound
Oxacycle
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

primary alcohol (CHEBI:63577 )
oxacycle (CHEBI:63577 )
monothioacetal (CHEBI:63577 )

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	-1.1	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	14.29	ChemAxon
pKa (Strongest Basic)	-0.16	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	55.16 m³·mol⁻¹	ChemAxon
Polarizability	21.7 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

HMDB0014847

DrugBank ID

DB00709

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

54812

KEGG Compound ID

C07065

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Lamivudine

METLIN ID

Not Available

PubChem Compound

60825

PDB ID

3TC

ChEBI ID

63577

Good Scents ID

Not Available

References

General References

Fox Z, Dragsted UB, Gerstoft J, Phillips AN, Kjaer J, Mathiesen L, Youle M, Katlama C, Hill A, Bruun JN, Clumeck N, Dellamonica P, Lundgren JD: A randomized trial to evaluate continuation versus discontinuation of lamivudine in individuals failing a lamivudine-containing regimen: the COLATE trial. Antivir Ther. 2006;11(6):761-70. [PubMed:17310820 ]
Papatheodoridis GV, Dimou E, Papadimitropoulos V: Nucleoside analogues for chronic hepatitis B: antiviral efficacy and viral resistance. Am J Gastroenterol. 2002 Jul;97(7):1618-28. doi: 10.1111/j.1572-0241.2002.05819.x. [PubMed:12135009 ]
Kuklenyik Z, Martin A, Pau CP, Holder A, Youngpairoj AS, Zheng Q, Cong ME, Garcia-Lerma JG, Heneine W, Pirkle JL, Barr JR: On-line coupling of anion exchange and ion-pair chromatography for measurement of intracellular triphosphate metabolites of reverse transcriptase inhibitors. J Chromatogr B Analyt Technol Biomed Life Sci. 2009 Nov 1;877(29):3659-66. doi: 10.1016/j.jchromb.2009.09.007. Epub 2009 Sep 11. [PubMed:19783232 ]
Rower JE, Klein B, Bushman LR, Anderson PL: Validation of a sensitive LC/MS/MS method for the determination of zidovudine and lamivudine in human plasma. Biomed Chromatogr. 2012 Jan;26(1):12-20. doi: 10.1002/bmc.1617. Epub 2011 Apr 4. [PubMed:21465499 ]
Shahabadi N, Maghsudi M, Mahdavi M, Pourfoulad M: Interaction of calf thymus DNA with the antiviral drug Lamivudine. DNA Cell Biol. 2012 Jan;31(1):122-7. doi: 10.1089/dna.2011.1228. Epub 2011 Jul 1. [PubMed:21721935 ]
LOTUS database [Link]

Showing NP-Card for 1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol (NP0328275)

MOL for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

3D MOL for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

3D SDF for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

3D-SDF for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

PDB for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

3D PDB for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

SMILES for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

INCHI for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

Structure for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)

3D Structure for NP0328275 (1-[(2r,5s)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-4-iminopyrimidin-2-ol)