MiMeDB: Showing metabocard for Kipukasin H (MMDBc0008730)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:28:32 UTC

Update Date

2022-08-31 06:28:57 UTC

Metabolite ID

MMDBc0008730

Metabolite Identification

Common Name

Kipukasin H

Description

Kipukasin H belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. Based on a literature review very few articles have been published on Kipukasin H.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152103282D          

 33 35  0  0  1  0            999 V2000
    0.6159   -1.8262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    0.6369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4189   -4.6572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9038   -3.9898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3403   -0.7643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1013    0.5947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9177   -1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4443   -1.0192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5118    0.0427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8859    0.3398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1331   -1.7840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5984   -4.5710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0574   -0.4672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -1.2991    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7982   -1.7840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0531   -2.5687    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8421   -0.7221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7477   -3.1499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2628   -3.8173    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5682   -3.2361    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5308   -2.0811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2964    0.2976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1135   -5.2384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -0.4741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4552   -0.1701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4122   -2.3962    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4990    0.8918    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8781   -2.5687    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0136   -1.5291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2621   -0.9692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7306   -0.9246    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2148   -2.3674    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4277   -3.3037    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  8  1  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  1  0  0  0
 12  3  1  0  0  0  0
 13  8  1  0  0  0  0
 13 10  2  0  0  0  0
 14 11  1  0  0  0  0
 15 14  1  0  0  0  0
 16 15  1  0  0  0  0
 17 13  1  0  0  0  0
 19 12  2  0  0  0  0
 19 18  1  0  0  0  0
 20  4  1  0  0  0  0
 16 20  1  1  0  0  0
 20 18  1  0  0  0  0
 21  7  1  0  0  0  0
 22  9  1  0  0  0  0
 23 12  1  0  0  0  0
 14 24  1  6  0  0  0
 25 17  2  0  0  0  0
 26 18  2  0  0  0  0
 27  2  1  0  0  0  0
 27 10  1  0  0  0  0
 28 11  1  0  0  0  0
 28 16  1  0  0  0  0
 15 29  1  6  0  0  0
 29 17  1  0  0  0  0
 11 30  1  6  0  0  0
 14 31  1  1  0  0  0
 15 32  1  1  0  0  0
 16 33  1  6  0  0  0
M  END


  Mrv1652305152103282D          

 33 35  0  0  1  0            999 V2000
    0.6159   -1.8262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    0.6369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4189   -4.6572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9038   -3.9898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3403   -0.7643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1013    0.5947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9177   -1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4443   -1.0192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5118    0.0427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8859    0.3398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1331   -1.7840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5984   -4.5710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0574   -0.4672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -1.2991    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7982   -1.7840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0531   -2.5687    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8421   -0.7221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7477   -3.1499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2628   -3.8173    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5682   -3.2361    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5308   -2.0811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2964    0.2976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1135   -5.2384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -0.4741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4552   -0.1701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4122   -2.3962    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4990    0.8918    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8781   -2.5687    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0136   -1.5291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2621   -0.9692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7306   -0.9246    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2148   -2.3674    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4277   -3.3037    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  8  1  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  1  0  0  0
 12  3  1  0  0  0  0
 13  8  1  0  0  0  0
 13 10  2  0  0  0  0
 14 11  1  0  0  0  0
 15 14  1  0  0  0  0
 16 15  1  0  0  0  0
 17 13  1  0  0  0  0
 19 12  2  0  0  0  0
 19 18  1  0  0  0  0
 20  4  1  0  0  0  0
 16 20  1  1  0  0  0
 20 18  1  0  0  0  0
 21  7  1  0  0  0  0
 22  9  1  0  0  0  0
 23 12  1  0  0  0  0
 14 24  1  6  0  0  0
 25 17  2  0  0  0  0
 26 18  2  0  0  0  0
 27  2  1  0  0  0  0
 27 10  1  0  0  0  0
 28 11  1  0  0  0  0
 28 16  1  0  0  0  0
 15 29  1  6  0  0  0
 29 17  1  0  0  0  0
 11 30  1  6  0  0  0
 14 31  1  1  0  0  0
 15 32  1  1  0  0  0
 16 33  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0008730

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=CC(O)=NC2=O)[C@]([H])(OC(=O)C2=C(OC)C=C(O)C=C2C)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C18H20N2O9/c1-8-5-9(22)6-10(27-2)13(8)17(25)29-15-14(24)11(7-21)28-16(15)20-4-3-12(23)19-18(20)26/h3-6,11,14-16,21-22,24H,7H2,1-2H3,(H,19,23,26)/t11-,14-,15-,16-/m1/s1

> <INCHI_KEY>
RARUJUZFKGDIOM-RAEVTNRLSA-N

> <FORMULA>
C18H20N2O9

> <MOLECULAR_WEIGHT>
408.363

> <EXACT_MASS>
408.116880232

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
38.71624165577475

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R,4R,5R)-4-hydroxy-2-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolan-3-yl 4-hydroxy-2-methoxy-6-methylbenzoate

> <ALOGPS_LOGP>
0.16

> <JCHEM_LOGP>
0.49974331333333394

> <ALOGPS_LOGS>
-2.37

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.671966464407744

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.145931476930845

> <JCHEM_PKA_STRONGEST_BASIC>
-2.980319758909687

> <JCHEM_POLAR_SURFACE_AREA>
158.34999999999997

> <JCHEM_REFRACTIVITY>
96.1946

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.76e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5R)-4-hydroxy-2-(4-hydroxy-2-oxopyrimidin-1-yl)-5-(hydroxymethyl)oxolan-3-yl 4-hydroxy-2-methoxy-6-methylbenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0       1.150  -3.409   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.263   1.189   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.515  -8.693   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.420  -7.448   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.635  -1.427   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.189   1.110   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.180  -2.854   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.829  -1.903   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.955   0.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.654   0.634   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.715  -3.330   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.984  -8.532   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.974  -0.872   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.469  -2.425   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.223  -3.330   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.699  -4.795   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.439  -1.348   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.262  -5.880   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       2.357  -7.126   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       4.794  -6.041   0.000  0.00  0.00           N+0
HETATM   21  O   UNK     0      10.324  -3.885   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -2.420   0.556   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       2.078  -9.778   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       6.469  -0.885   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.583  -0.317   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       2.636  -4.473   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       2.798   1.665   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       7.239  -4.795   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       3.759  -2.854   0.000  0.00  0.00           O+0
HETATM   30  H   UNK     0       7.956  -1.809   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0       5.097  -1.726   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       4.134  -4.419   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0       6.398  -6.167   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2   27                                                            
CONECT    3    4   12                                                       
CONECT    4    3   20                                                       
CONECT    5    8    9                                                       
CONECT    6    9   10                                                       
CONECT    7   11   21                                                       
CONECT    8    1    5   13                                                  
CONECT    9    5    6   22                                                  
CONECT   10    6   13   27                                                  
CONECT   11    7   14   28   30                                             
CONECT   12    3   19   23                                                  
CONECT   13    8   10   17                                                  
CONECT   14   11   15   24   31                                             
CONECT   15   14   16   29   32                                             
CONECT   16   15   20   28   33                                             
CONECT   17   13   25   29                                                  
CONECT   18   19   20   26                                                  
CONECT   19   12   18                                                       
CONECT   20    4   16   18                                                  
CONECT   21    7                                                            
CONECT   22    9                                                            
CONECT   23   12                                                            
CONECT   24   14                                                            
CONECT   25   17                                                            
CONECT   26   18                                                            
CONECT   27    2   10                                                       
CONECT   28   11   16                                                       
CONECT   29   15   17                                                       
CONECT   30   11                                                            
CONECT   31   14                                                            
CONECT   32   15                                                            
CONECT   33   16                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

Synonyms

Not Available

Molecular Formula

C₁₈H₂₀N₂O₉

Average Mass

408.363

Monoisotopic Mass

408.116880232

IUPAC Name

(2R,3R,4R,5R)-4-hydroxy-2-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolan-3-yl 4-hydroxy-2-methoxy-6-methylbenzoate

Traditional Name

(2R,3R,4R,5R)-4-hydroxy-2-(4-hydroxy-2-oxopyrimidin-1-yl)-5-(hydroxymethyl)oxolan-3-yl 4-hydroxy-2-methoxy-6-methylbenzoate

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=CC(O)=NC2=O)[C@]([H])(OC(=O)C2=C(OC)C=C(O)C=C2C)[C@]1([H])O

InChI Identifier

InChI=1S/C18H20N2O9/c1-8-5-9(22)6-10(27-2)13(8)17(25)29-15-14(24)11(7-21)28-16(15)20-4-3-12(23)19-18(20)26/h3-6,11,14-16,21-22,24H,7H2,1-2H3,(H,19,23,26)/t11-,14-,15-,16-/m1/s1

InChI Key

RARUJUZFKGDIOM-RAEVTNRLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
Glycosyl compound
N-glycosyl compound
O-methoxybenzoic acid or derivatives
Benzoate ester
Methoxyphenol
Pentose monosaccharide
Benzoic acid or derivatives
Anisole
Phenoxy compound
Benzoyl
M-cresol
Phenol ether
Methoxybenzene
Toluene
Alkyl aryl ether
Pyrimidone
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyrimidine
Monosaccharide
Monocyclic benzene moiety
Benzenoid
Hydropyrimidine
Heteroaromatic compound
Vinylogous amide
Oxolane
Carboxylic acid ester
Lactam
Secondary alcohol
Urea
Organoheterocyclic compound
Carboxylic acid derivative
Azacycle
Ether
Oxacycle
Primary alcohol
Organic oxygen compound
Alcohol
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.76 g/L	ALOGPS
logP	0.16	ALOGPS
logP	0.5	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	7.15	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	158.35 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	96.19 m³·mol⁻¹	ChemAxon
Polarizability	38.72 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

22842426

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23786324

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Kipukasin H (MMDBc0008730)

MOL for #<Metabolite:0x00007f9235ccc760>

3D MOL for #<Metabolite:0x00007f9235ccc760>

3D SDF for #<Metabolite:0x00007f9235ccc760>

3D-SDF for #<Metabolite:0x00007f9235ccc760>

PDB for #<Metabolite:0x00007f9235ccc760>

3D PDB for #<Metabolite:0x00007f9235ccc760>

SMILES for #<Metabolite:0x00007f9235ccc760>

INCHI for #<Metabolite:0x00007f9235ccc760>

Structure for #<Metabolite:0x00007f9235ccc760>

3D Structure for #<Metabolite:0x00007f9235ccc760>