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Showing NP-Card for 4-imino-1-methylpyrimidine-2,5-diol (NP0203672)

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Record Information
Version2.0
Created at2022-09-04 23:11:27 UTC
Updated at2022-09-04 23:11:27 UTC
NP-MRD IDNP0203672
Secondary Accession NumbersNone
Natural Product Identification
Common Name4-imino-1-methylpyrimidine-2,5-diol
Description5-Hydroxy-methylcytosine belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 4-imino-1-methylpyrimidine-2,5-diol was first documented in 2017 (PMID: 28661477). Based on a literature review a significant number of articles have been published on 5-hydroxy-methylcytosine (PMID: 34884685) (PMID: 33440144) (PMID: 33312403) (PMID: 32344274) (PMID: 31796828) (PMID: 30542593).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0203672 (4-imino-1-methylpyrimidine-2,5-diol)


  Mrv1652309052201112D          

 10 10  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0203672 (4-imino-1-methylpyrimidine-2,5-diol)

     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
    3.4825    1.3483    0.1518 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5792    1.8204    0.2863 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4888    1.1226    0.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2771    1.6870    0.3382 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8727    0.9724    0.2231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1247    1.5779    0.3988 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8632   -0.3419   -0.0632 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1122   -1.0683   -0.1774 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3263   -0.9393   -0.2350 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5207   -0.2272   -0.1220 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7478   -0.8459   -0.2997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1672    2.4720    0.8212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9795   -2.1551   -0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7779   -0.7557    0.6756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6634   -0.8437   -1.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3304   -1.9907   -0.4639 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8081   -1.8330   -0.5166 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 10  3  1  0
  3  2  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  5  7  1  0
  8 13  1  0
  8 14  1  0
  8 15  1  0
  9 16  1  0
 11 17  1  0
  2  1  1  0
  6 12  1  0
M  END
Download

3D SDF for NP0203672 (4-imino-1-methylpyrimidine-2,5-diol)


  Mrv1652309052201112D          

 10 10  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0203672

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=C(O)C(=N)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H7N3O2/c1-8-2-3(9)4(6)7-5(8)10/h2,9H,1H3,(H2,6,7,10)

> <INCHI_KEY>
KHJMGTNWGFHSJU-UHFFFAOYSA-N

> <FORMULA>
C5H7N3O2

> <MOLECULAR_WEIGHT>
141.13

> <EXACT_MASS>
141.053826477

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.967859416951427

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-imino-1-methyl-1,4-dihydropyrimidine-2,5-diol

> <JCHEM_LOGP>
-0.2825769646666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.271445552722048

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.017752537137747

> <JCHEM_PKA_STRONGEST_BASIC>
1.3396887530794495

> <JCHEM_POLAR_SURFACE_AREA>
79.91

> <JCHEM_REFRACTIVITY>
46.2251

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-imino-1-methylpyrimidine-2,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0203672 (4-imino-1-methylpyrimidine-2,5-diol)

Download
PDB for NP0203672 (4-imino-1-methylpyrimidine-2,5-diol)
HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8    2   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0203672 (4-imino-1-methylpyrimidine-2,5-diol)
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SMILES for NP0203672 (4-imino-1-methylpyrimidine-2,5-diol)
CN1C=C(O)C(=N)N=C1O
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INCHI for NP0203672 (4-imino-1-methylpyrimidine-2,5-diol)
InChI=1S/C5H7N3O2/c1-8-2-3(9)4(6)7-5(8)10/h2,9H,1H3,(H2,6,7,10)
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H7N3O2
Average Mass141.1300 Da
Monoisotopic Mass141.05383 Da
IUPAC Name4-imino-1-methyl-1,4-dihydropyrimidine-2,5-diol
Traditional Name4-imino-1-methylpyrimidine-2,5-diol
CAS Registry NumberNot Available
SMILES
CN1C=C(O)C(=N)N=C1O
InChI Identifier
InChI=1S/C5H7N3O2/c1-8-2-3(9)4(6)7-5(8)10/h2,9H,1H3,(H2,6,7,10)
InChI KeyKHJMGTNWGFHSJU-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassDiazines  
Sub ClassPyrimidines and pyrimidine derivatives  
Direct ParentHydroxypyrimidines  
Alternative Parents
Substituents
  • Aminopyrimidine
    • 

  • Pyrimidone
    • 

  • Hydroxypyrimidine
    • 

  • Hydropyrimidine
    • 

  • Imidolactam
    • 

  • Heteroaromatic compound
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.28ChemAxon
pKa (Strongest Acidic)6.02ChemAxon
pKa (Strongest Basic)1.34ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area79.91 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity46.23 m³·mol⁻¹ChemAxon
Polarizability12.97 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID19615876  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound20778715  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Walsh SW, Al Dulaimi M, Archer KJ, Strauss JF 3rd: Patterns of Maternal Neutrophil Gene Expression at 30 Weeks of Gestation, but Not DNA Methylation, Distinguish Mild from Severe Preeclampsia. Int J Mol Sci. 2021 Nov 28;22(23):12876. doi: 10.3390/ijms222312876. [PubMed:34884685  ] 
  2. Banks KM, Lan Y, Evans T: Tet Proteins Regulate Neutrophil Granulation in Zebrafish through Demethylation of socs3b mRNA. Cell Rep. 2021 Jan 12;34(2):108632. doi: 10.1016/j.celrep.2020.108632. [PubMed:33440144  ] 
  3. Cheng XJ, Guan FL, Li Q, Dai G, Li HF, Li XK: AlCl(3) exposure regulates neuronal development by modulating DNA modification. World J Stem Cells. 2020 Nov 26;12(11):1354-1365. doi: 10.4252/wjsc.v12.i11.1354. [PubMed:33312403  ] 
  4. Wang Y, Liu Q, Kang J, Zhang Y, Quan F: Overexpression of PGC7 in donor cells maintains the DNA methylation status of imprinted genes in goat embryos derived from somatic cell nuclear transfer technology. Theriogenology. 2020 Jul 15;151:86-94. doi: 10.1016/j.theriogenology.2020.04.013.  Epub 2020 Apr 15. [PubMed:32344274  ] 
  5. Rocha MA, Veronezi GMB, Felisbino MB, Gatti MSV, Tamashiro WMSC, Mello MLS: Sodium valproate and 5-aza-2'-deoxycytidine differentially modulate DNA demethylation in G1 phase-arrested and proliferative HeLa cells. Sci Rep. 2019 Dec 3;9(1):18236. doi: 10.1038/s41598-019-54848-x. [PubMed:31796828  ] 
  6. Torabifard H, Cisneros GA: Insight into wild-type and T1372E TET2-mediated 5hmC oxidation using ab initio QM/MM calculations. Chem Sci. 2018 Sep 11;9(44):8433-8445. doi: 10.1039/c8sc02961j. eCollection 2018  Nov 28. [PubMed:30542593  ] 
  7. Zhang X, Chen X, Weirauch MT, Zhang X, Burleson JD, Brandt EB, Ji H: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome. Environ Epigenet. 2018 Jul 27;4(3):dvy020. doi: 10.1093/eep/dvy020. eCollection  2018 Jul. [PubMed:30090644  ] 
  8. Moran B, Silva R, Perry AS, Gallagher WM: Epigenetics of malignant melanoma. Semin Cancer Biol. 2018 Aug;51:80-88. doi: 10.1016/j.semcancer.2017.10.006. Epub  2017 Oct 23. [PubMed:29074395  ] 
  9. Chen Q, Yin D, Zhang Y, Yu L, Li XD, Zhou ZJ, Zhou SL, Gao DM, Hu J, Jin C, Wang Z, Shi YH, Cao Y, Fan J, Dai Z, Zhou J: MicroRNA-29a induces loss of 5-hydroxymethylcytosine and promotes metastasis of hepatocellular carcinoma through a TET-SOCS1-MMP9 signaling axis. Cell Death Dis. 2017 Jun 29;8(6):e2906. doi: 10.1038/cddis.2017.142. [PubMed:28661477  ] 
  10. Yan H, Wang Y, Qu X, Li J, Hale J, Huang Y, An C, Papoin J, Guo X, Chen L, Kang Q, Li W, Schulz VP, Gallagher PG, Hillyer CD, Mohandas N, An X: Distinct roles for TET family proteins in regulating human erythropoiesis. Blood. 2017 Apr 6;129(14):2002-2012. doi: 10.1182/blood-2016-08-736587. Epub 2017  Feb 6. [PubMed:28167661  ] 
  11. LOTUS database [Link]