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Showing NP-Card for 1,3-Dimethylurea (NP0002662)

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Record Information
Version1.0
Created at2020-11-23 18:26:20 UTC
Updated at2021-08-19 23:59:14 UTC
NP-MRD IDNP0002662
Secondary Accession NumbersNone
Natural Product Identification
Common Name1,3-Dimethylurea
Provided ByBMRBBMRB logo
DescriptionDimethylurea belongs to the class of organic compounds known as ureas. Ureas are compounds containing two amine groups joined by a carbonyl (C=O) functional group. Dimethylurea is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on Dimethylurea (PMID: 34404046) (PMID: 34403937) (PMID: 34403896) (PMID: 34403832) (PMID: 34403816) (PMID: 34403725).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002662 (1,3-Dimethylurea)


     RDKit          2D

 14 13  0  0  0  0  0  0  0  0999 V2000
    2.1061    0.5422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4630   -0.8129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0322   -0.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6753   -2.2886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8842    0.3010    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3794    0.1804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4612   -0.1009    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7509    1.1854    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7492    1.8974    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3150   -2.0474    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2411    1.6562    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2588   -1.3147    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5000    1.6756    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8745    0.0598    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
  3  5  1  0
  5  6  1  0
  1  7  1  1
  1  8  1  0
  1  9  1  0
  2 10  1  0
  5 11  1  0
  6 12  1  1
  6 13  1  0
  6 14  1  0
M  END
Download

3D MOL for NP0002662 (1,3-Dimethylurea)

NP0002662
     RDKit          3D

 14 13  0  0  0  0  0  0  0  0999 V2000
    2.4564   -0.1558    0.3754 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2731    0.3943   -0.2102 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0257   -0.1078    0.0775 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0981   -1.0733    0.8822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1984    0.4238   -0.4913 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4780   -0.1305   -0.1577 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9481   -0.9020   -0.2923 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1527    0.7087    0.5699 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2110   -0.6570    1.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3526    1.1914   -0.8725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1367    1.2125   -1.1484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3050    0.6018   -0.1942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7449   -1.0159   -0.8064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4071   -0.4903    0.9105 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
  3  5  1  0
  5  6  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  5 11  1  0
  6 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

3D SDF for NP0002662 (1,3-Dimethylurea)


     RDKit          2D

 14 13  0  0  0  0  0  0  0  0999 V2000
    2.1061    0.5422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4630   -0.8129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0322   -0.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6753   -2.2886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8842    0.3010    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3794    0.1804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4612   -0.1009    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7509    1.1854    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7492    1.8974    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3150   -2.0474    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2411    1.6562    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2588   -1.3147    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5000    1.6756    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8745    0.0598    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
  3  5  1  0
  5  6  1  0
  1  7  1  1
  1  8  1  0
  1  9  1  0
  2 10  1  0
  5 11  1  0
  6 12  1  1
  6 13  1  0
  6 14  1  0
M  END
> <DATABASE_ID>
NP0002662

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CNC(=O)NC

> <INCHI_IDENTIFIER>
InChI=1S/C3H8N2O/c1-4-3(6)5-2/h1-2H3,(H2,4,5,6)

> <INCHI_KEY>
MGJKQDOBUOMPEZ-UHFFFAOYSA-N

> <FORMULA>
C3H8N2O

> <MOLECULAR_WEIGHT>
88.1084

> <EXACT_MASS>
88.063662888

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
9.132914389601591

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-dimethylurea

> <ALOGPS_LOGP>
-1.27

> <JCHEM_LOGP>
-0.9164817303333335

> <ALOGPS_LOGS>
0.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.624730435299757

> <JCHEM_PKA_STRONGEST_BASIC>
-2.014941993847047

> <JCHEM_POLAR_SURFACE_AREA>
41.129999999999995

> <JCHEM_REFRACTIVITY>
22.936

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.65e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dimethylurea

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002662 (1,3-Dimethylurea)

NP0002662
     RDKit          3D

 14 13  0  0  0  0  0  0  0  0999 V2000
    2.4564   -0.1558    0.3754 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2731    0.3943   -0.2102 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0257   -0.1078    0.0775 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0981   -1.0733    0.8822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1984    0.4238   -0.4913 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4780   -0.1305   -0.1577 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9481   -0.9020   -0.2923 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1527    0.7087    0.5699 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2110   -0.6570    1.3574 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3526    1.1914   -0.8725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1367    1.2125   -1.1484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3050    0.6018   -0.1942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7449   -1.0159   -0.8064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4071   -0.4903    0.9105 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
  3  5  1  0
  5  6  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  5 11  1  0
  6 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

PDB for NP0002662 (1,3-Dimethylurea)

HEADER    PROTEIN                                 14-MAY-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-12         0                                  
HETATM    1  N   UNK     0      34.478 -28.771   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      33.227 -27.911   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      31.976 -28.771   0.000  0.00  0.00           N+0
HETATM    4  O   UNK     0      33.227 -26.269   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      30.569 -28.145   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      35.911 -28.087   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2    5                                                       
CONECT    4    2                                                            
CONECT    5    3                                                            
CONECT    6    1                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for NP0002662 (1,3-Dimethylurea)

COMPND    NP0002662
HETATM    1  C1  UNL     1       2.456  -0.156   0.375  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.273   0.394  -0.210  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.026  -0.108   0.078  1.00  0.00           C  
HETATM    4  O1  UNL     1      -0.098  -1.073   0.882  1.00  0.00           O  
HETATM    5  N2  UNL     1      -1.198   0.424  -0.491  1.00  0.00           N  
HETATM    6  C3  UNL     1      -2.478  -0.131  -0.158  1.00  0.00           C  
HETATM    7  H1  UNL     1       2.948  -0.902  -0.292  1.00  0.00           H  
HETATM    8  H2  UNL     1       3.153   0.709   0.570  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.211  -0.657   1.357  1.00  0.00           H  
HETATM   10  H4  UNL     1       1.353   1.191  -0.873  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.137   1.213  -1.148  1.00  0.00           H  
HETATM   12  H6  UNL     1      -3.305   0.602  -0.194  1.00  0.00           H  
HETATM   13  H7  UNL     1      -2.745  -1.016  -0.806  1.00  0.00           H  
HETATM   14  H8  UNL     1      -2.407  -0.490   0.911  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10
CONECT    3    4    4    5
CONECT    5    6   11
CONECT    6   12   13   14
END
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SMILES for NP0002662 (1,3-Dimethylurea)

CNC(=O)NC
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INCHI for NP0002662 (1,3-Dimethylurea)

InChI=1S/C3H8N2O/c1-4-3(6)5-2/h1-2H3,(H2,4,5,6)
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View in JSmol
Synonyms
ValueSource
1,3-DimethylureaChEBI
N,N'-dimethylureaHMDB
N,N-Dimethyl-ureaHMDB
Chemical FormulaC3H8N2O
Average Mass88.1084 Da
Monoisotopic Mass88.06366 Da
IUPAC Name1,3-dimethylurea
Traditional Namedimethylurea
CAS Registry NumberNot Available
SMILES
CNC(=O)NC
InChI Identifier
InChI=1S/C3H8N2O/c1-4-3(6)5-2/h1-2H3,(H2,4,5,6)
InChI KeyMGJKQDOBUOMPEZ-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ureas. Ureas are compounds containing two amine groups joined by a carbonyl (C=O) functional group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic carbonic acids and derivatives
Sub ClassUreas
Direct ParentUreas
Alternative ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting Point108.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Boiling Point269.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility16150 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.490The Good Scents Company Information System
Predicted Properties
PropertyValueSource
logP-1.3ALOGPS
logP-0.92ChemAxon
logS0.27ALOGPS
pKa (Strongest Acidic)15.62ChemAxon
pKa (Strongest Basic)-2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area41.13 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity22.94 m³·mol⁻¹ChemAxon
Polarizability9.13 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0029198
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID7021
KEGG Compound IDC16364
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDimethylurea
METLIN IDNot Available
PubChem Compound7293
PDB IDMMU
ChEBI ID80472
Good Scents IDrw1147651
References
General References
  1. 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 ]
  2. Al Riyees L, Al Madani W, Firwana N, Balkhy HH, Ferwana M, Alkhudhayri A: Antibiotic Prophylaxis against Surgical Site Infection after Open Hernia Surgery: A Systematic Review and Meta-Analysis. Eur Surg Res. 2021 Aug 17:1-13. doi: 10.1159/000517404. [PubMed:34404046 ]
  3. Bashir B, Shahid W, Ashraf M, Saleem M, Aziz-Ur-Rehman, Muzaffar S, Imran M, Amjad H, Bhattarai K, Riaz N: Identification of phenylcarbamoylazinane-1,3,4-oxadiazole amides as lipoxygenase inhibitors with expression analysis and in silico studies. Bioorg Chem. 2021 Aug 4;115:105243. doi: 10.1016/j.bioorg.2021.105243. [PubMed:34403937 ]
  4. Mavrommatis A, Theodorou G, Politis I, Tsiplakou E: Schizochytrium sp. Dietary supplementation modify Toll-like receptor 4 (TLR4) transcriptional regulation in monocytes and neutrophils of dairy goats. Cytokine. 2021 Aug 13;148:155588. doi: 10.1016/j.cyto.2021.155588. [PubMed:34403896 ]
  5. Laiton-Donato K, Franco-Munoz C, Alvarez-Diaz DA, Ruiz-Moreno HA, Usme-Ciro JA, Prada DA, Reales-Gonzalez J, Corchuelo S, Herrera-Sepulveda MT, Naizaque J, Santamaria G, Rivera J, Rojas P, Ortiz JH, Cardona A, Malo D, Prieto-Alvarado F, Gomez FR, Wiesner M, Martinez MLO, Mercado-Reyes M: Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Infect Genet Evol. 2021 Aug 14:105038. doi: 10.1016/j.meegid.2021.105038. [PubMed:34403832 ]
  6. Maverakis E, Merleev AA, Park D, Kailemia MJ, Xu G, Ruhaak LR, Kim K, Hong Q, Li Q, Leung P, Liakos W, Wan YY, Bowlus CL, Marusina AI, Lal NN, Xie Y, Luxardi G, Lebrilla CB: Glycan biomarkers of autoimmunity and bile acid-associated alterations of the human glycome: Primary biliary cirrhosis and primary sclerosing cholangitis-specific glycans. Clin Immunol. 2021 Aug 14:108825. doi: 10.1016/j.clim.2021.108825. [PubMed:34403816 ]
  7. Lee D, Kim JY, Qi Y, Park S, Lee HL, Yamabe N, Kim H, Jang DS, Kang KS: Phytochemicals from the Flowers of Prunus persica (L.) Batsch: Anti-adipogenic Effect of Mandelamide on 3T3-L1 preadipocytes. Bioorg Med Chem Lett. 2021 Aug 14:128326. doi: 10.1016/j.bmcl.2021.128326. [PubMed:34403725 ]
  8. Sasaki Y, Zhu J, Shi Y, Gu W, Kobe B, Ve T, DiAntonio A, Milbrandt J: Nicotinic acid mononucleotide is an allosteric SARM1 inhibitor promoting axonal protection. Exp Neurol. 2021 Aug 14:113842. doi: 10.1016/j.expneurol.2021.113842. [PubMed:34403688 ]
  9. Rong MK, Bobylev EO, Holtrop F, Nieger M, Ehlers AW, Slootweg JC, Lammertsma K: Atypical And Asymmetric 1,3-P,N-Ligands: The Synthesis, Coordination and Catalytic Performance of Cycloiminophosphanes. Chemistry. 2021 Aug 17. doi: 10.1002/chem.202101921. [PubMed:34403555 ]
  10. Gouda A, Tolba SA, El-Moniary MM: Zinc and L-Ascorbic Acid Dietary Supplementation Affected Antioxidant Status, Heat Shock Protein 70, and Some Immunoglobulins in Japanese Quail Under Heat Stress Conditions. Biol Trace Elem Res. 2021 Aug 17. pii: 10.1007/s12011-021-02884-y. doi: 10.1007/s12011-021-02884-y. [PubMed:34403050 ]
  11. Hoppe C, Freuding M, Buntzel J, Munstedt K, Hubner J: Clinical efficacy and safety of oral and intravenous vitamin C use in patients with malignant diseases. J Cancer Res Clin Oncol. 2021 Aug 17. pii: 10.1007/s00432-021-03759-4. doi: 10.1007/s00432-021-03759-4. [PubMed:34402972 ]
  12. Studer JM, Kiefer ZE, Goetz BM, Keating AF, Baumgard LH, Rambo ZJ, Schweer WP, Wilson ME, Rapp C, Ross JW: Evaluation of the molecular response of corpora lutea to manganese amino acid complex supplementation in gilts. J Anim Sci. 2021 Aug 17. pii: 6353575. doi: 10.1093/jas/skab245. [PubMed:34402900 ]
  13. Chakraborty A, Mitra A, Tawate M, Sahoo S, Lad S, Rakshit S, Gaikwad S, Basu S, Shimpi H, Banerjee S: Therapeutic Multidose Preparation of a Ready-to-Use (177)Lu-PSMA-617 Using Carrier Added Lutetium-177 in a Hospital Radiopharmacy and Its Clinical Efficacy. Cancer Biother Radiopharm. 2021 Aug 16. doi: 10.1089/cbr.2020.4261. [PubMed:34402687 ]