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Showing NP-Card for n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid (NP0327646)

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Record Information
Version2.0
Created at2022-09-12 10:25:25 UTC
Updated at2022-09-12 10:25:25 UTC
NP-MRD IDNP0327646
Secondary Accession NumbersNone
Natural Product Identification
Common Namen-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid
Description n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid is found in Allium tuberosum, Arabidopsis thaliana, Aristolochia kaempferi, Gynostemma pentaphyllum and Rhinacanthus nasutus.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0327646 (n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid)

 
  Mrv1533006041517142D          
 
 11 11  0  0  1  0            999 V2000
   18.2325   -9.1575    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.5212   -8.3737    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4075   -9.1575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7275   -9.8175    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.8200   -7.8787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1600   -8.3737    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.9125   -9.8175    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.5525   -9.8175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8200   -7.0537    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0475  -10.4362    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.8825   -9.0750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  1  0  0  0  0
  5  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 11  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
Download

3D MOL for NP0327646 (n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid)

     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
    2.9840   -0.5892    0.6677 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9248   -0.6309   -0.2666 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1392   -1.1037   -1.4048 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6615   -0.1544    0.0708 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4861   -0.1532   -0.8136 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9776    1.1967   -0.8685 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8193    1.4035    0.2417 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2084    2.5015    0.7684 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1955    0.0930    0.7190 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5723   -0.8671   -0.1133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8751   -2.0526   -0.2282 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7780    0.0759    0.5375 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0053   -1.2126    1.5046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4808    0.2454    1.0336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2561   -0.5771   -1.8049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7542    1.8932   -1.5930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8289   -0.0685    1.5497 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10  5  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  5 15  1  6
  6 16  1  0
  9 17  1  0
M  END
Download

3D SDF for NP0327646 (n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid)

 
  Mrv1533006041517142D          
 
 11 11  0  0  1  0            999 V2000
   18.2325   -9.1575    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.5212   -8.3737    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4075   -9.1575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7275   -9.8175    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.8200   -7.8787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1600   -8.3737    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.9125   -9.8175    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.5525   -9.8175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8200   -7.0537    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0475  -10.4362    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.8825   -9.0750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  1  0  0  0  0
  5  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 11  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0327646

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H6N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h1H,(H3,5,6,10)(H2,7,8,9,11)/t1-/m1/s1

> <INCHI_KEY>
POJWUDADGALRAB-PVQJCKRUSA-N

> <FORMULA>
C4H6N4O3

> <MOLECULAR_WEIGHT>
158.117

> <EXACT_MASS>
158.043990069

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.95330447072138

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(4R)-2,5-dioxoimidazolidin-4-yl]urea

> <ALOGPS_LOGP>
-1.95

> <JCHEM_LOGP>
-2.360540882

> <ALOGPS_LOGS>
-1.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.41419987137925

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.948848806915678

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3762243606061957

> <JCHEM_POLAR_SURFACE_AREA>
113.32

> <JCHEM_REFRACTIVITY>
32.02250000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.73e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-allantoin

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0327646 (n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid)

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PDB for NP0327646 (n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid)
HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      34.034 -17.094   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      34.573 -15.631   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      32.494 -17.094   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      34.958 -18.326   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      33.264 -14.707   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      32.032 -15.631   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      31.570 -18.326   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      36.498 -18.326   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      33.264 -13.167   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      37.422 -19.481   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0      37.114 -16.940   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6    7                                                  
CONECT    4    1    8                                                       
CONECT    5    2    9    6                                                  
CONECT    6    3    5                                                       
CONECT    7    3                                                            
CONECT    8    4   10   11                                                  
CONECT    9    5                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0327646 (n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid)
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SMILES for NP0327646 (n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid)
NC(=O)N[C@@H]1NC(=O)NC1=O
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INCHI for NP0327646 (n-[(4r)-2,5-dihydroxy-4h-imidazol-4-yl]carbamimidic acid)
InChI=1S/C4H6N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h1H,(H3,5,6,10)(H2,7,8,9,11)/t1-/m1/s1
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View in JSmol
Synonyms
ValueSource
(R)(-)-AllantoinChEBI
(R)-AllantoinChEBI
Chemical FormulaC4H6N4O3
Average Mass158.1170 Da
Monoisotopic Mass158.04399 Da
IUPAC Name[(4R)-2,5-dioxoimidazolidin-4-yl]urea
Traditional Name(R)-allantoin
CAS Registry NumberNot Available
SMILES
NC(=O)N[C@@H]1NC(=O)NC1=O
InChI Identifier
InChI=1S/C4H6N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h1H,(H3,5,6,10)(H2,7,8,9,11)/t1-/m1/s1
InChI KeyPOJWUDADGALRAB-PVQJCKRUSA-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 Origin
Species NameSourceReference
Allium tuberosumLOTUS Database
Arabidopsis thalianaLOTUS Database
Aristolochia kaempferiLOTUS Database
Gynostemma pentaphyllumLOTUS Database
Rhinacanthus nasutusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as allantoins. These are heterocyclic compounds containing an imiazolidine ring substituted by a ketone group at positions 2 and 5, and an urea at position 4.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassAzolidines  
Sub ClassImidazolidines  
Direct ParentAllantoins  
Alternative Parents
Substituents
  • Allantoin
    • 

  • Alpha-amino acid or derivatives
    • 

  • 5-monosubstituted hydantoin
    • 

  • N-acyl urea
    • 

  • Ureide
    • 

  • Dicarboximide
    • 

  • Carbonic acid derivative
    • 

  • Urea
    • 

  • Carboxylic acid derivative
    • 

  • Azacycle
    • 

  • Organonitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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-2ALOGPS
logP-2.4ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)7.95ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area113.32 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.02 m³·mol⁻¹ChemAxon
Polarizability12.95 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 IDNot Available
KEGG Compound IDC02348  
BioCyc IDR--ALLANTOIN  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439713  
PDB IDNot Available
ChEBI ID15677  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]