NP-MRD: Showing NP-Card for Cytogenin (NP0010916)

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Record Information

Version

2.0

Created at

2021-01-05 20:42:57 UTC

Updated at

2021-07-15 17:07:26 UTC

NP-MRD ID

NP0010916

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytogenin

Provided By

NPAtlas

Description

Cytogenin is found in Streptomyces eurocidicus. Cytogenin was first documented in 1990 (PMID: 2272926). Based on a literature review very few articles have been published on Cytogenin.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242107423D          

 26 27  0  0  0  0            999 V2000
    3.8720   -1.6376    0.0191 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5498   -0.2974    0.2491 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2600    0.2075    0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0404    1.5419    0.4658 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7738    2.1349    0.4634 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6839    3.4681    0.7135 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3211    1.3384    0.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6157    1.8576    0.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8194    3.0729    0.4050 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6347    1.0634   -0.0601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4979   -0.2212   -0.2965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7104   -1.0410   -0.5678 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3444   -2.3624   -0.7911 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2370   -0.7819   -0.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1199   -0.0117   -0.0356 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1422   -0.5565   -0.0242 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8518   -1.8971    0.4703 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1173   -2.2590    0.5785 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9009   -1.9122   -1.0463 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9008    2.1659    0.6665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0023    4.1194    0.7762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2161   -0.6652   -1.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4450   -0.9603    0.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3297   -2.9180    0.0086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -1.8344   -0.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2830   -1.6138   -0.2161 H   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
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16  3  1  0  0  0  0
 15  7  1  0  0  0  0
  1 17  1  0  0  0  0
  1 18  1  0  0  0  0
  1 19  1  0  0  0  0
  4 20  1  0  0  0  0
  6 21  1  0  0  0  0
 12 22  1  0  0  0  0
 12 23  1  0  0  0  0
 13 24  1  0  0  0  0
 14 25  1  0  0  0  0
 16 26  1  0  0  0  0
M  END


  Mrv1652306242107423D          

 26 27  0  0  0  0            999 V2000
    3.8720   -1.6376    0.0191 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5498   -0.2974    0.2491 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2600    0.2075    0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0404    1.5419    0.4658 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7738    2.1349    0.4634 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6839    3.4681    0.7135 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3211    1.3384    0.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6157    1.8576    0.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8194    3.0729    0.4050 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6347    1.0634   -0.0601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4979   -0.2212   -0.2965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7104   -1.0410   -0.5678 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3444   -2.3624   -0.7911 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2370   -0.7819   -0.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1199   -0.0117   -0.0356 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1422   -0.5565   -0.0242 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8518   -1.8971    0.4703 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1173   -2.2590    0.5785 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9009   -1.9122   -1.0463 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9008    2.1659    0.6665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0023    4.1194    0.7762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2161   -0.6652   -1.4857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4450   -0.9603    0.2574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3297   -2.9180    0.0086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0823   -1.8344   -0.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2830   -1.6138   -0.2161 H   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
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16  3  1  0  0  0  0
 15  7  1  0  0  0  0
  1 17  1  0  0  0  0
  1 18  1  0  0  0  0
  1 19  1  0  0  0  0
  4 20  1  0  0  0  0
  6 21  1  0  0  0  0
 12 22  1  0  0  0  0
 12 23  1  0  0  0  0
 13 24  1  0  0  0  0
 14 25  1  0  0  0  0
 16 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0010916

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C2C(=O)OC(=C([H])C2=C([H])C(OC([H])([H])[H])=C1[H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C11H10O5/c1-15-7-2-6-3-8(5-12)16-11(14)10(6)9(13)4-7/h2-4,12-13H,5H2,1H3

> <INCHI_KEY>
CAWNOJXNAUEIGB-UHFFFAOYSA-N

> <FORMULA>
C11H10O5

> <MOLECULAR_WEIGHT>
222.196

> <EXACT_MASS>
222.052823422

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
21.409990709128095

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-hydroxy-3-(hydroxymethyl)-6-methoxy-1H-isochromen-1-one

> <ALOGPS_LOGP>
1.28

> <JCHEM_LOGP>
1.3973164873333332

> <ALOGPS_LOGS>
-2.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.357921477487558

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.468248109780562

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0799410374820964

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
57.2929

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.90e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-hydroxy-3-(hydroxymethyl)-6-methoxyisochromen-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       3.872  -1.638   0.019  0.00  0.00           C+0
HETATM    2  O   UNK     0       3.550  -0.297   0.249  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.260   0.208   0.227  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.040   1.542   0.466  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.774   2.135   0.463  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.684   3.468   0.714  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.321   1.338   0.208  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.616   1.858   0.188  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.819   3.073   0.405  0.00  0.00           O+0
HETATM   10  O   UNK     0      -2.635   1.063  -0.060  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.498  -0.221  -0.297  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.710  -1.041  -0.568  0.00  0.00           C+0
HETATM   13  O   UNK     0      -3.344  -2.362  -0.791  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.237  -0.782  -0.288  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.120  -0.012  -0.036  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.142  -0.557  -0.024  0.00  0.00           C+0
HETATM   17  H   UNK     0       4.852  -1.897   0.470  0.00  0.00           H+0
HETATM   18  H   UNK     0       3.117  -2.259   0.579  0.00  0.00           H+0
HETATM   19  H   UNK     0       3.901  -1.912  -1.046  0.00  0.00           H+0
HETATM   20  H   UNK     0       2.901   2.166   0.667  0.00  0.00           H+0
HETATM   21  H   UNK     0      -0.002   4.119   0.776  0.00  0.00           H+0
HETATM   22  H   UNK     0      -4.216  -0.665  -1.486  0.00  0.00           H+0
HETATM   23  H   UNK     0      -4.445  -0.960   0.257  0.00  0.00           H+0
HETATM   24  H   UNK     0      -3.330  -2.918   0.009  0.00  0.00           H+0
HETATM   25  H   UNK     0      -1.082  -1.834  -0.478  0.00  0.00           H+0
HETATM   26  H   UNK     0       1.283  -1.614  -0.216  0.00  0.00           H+0
CONECT    1    2   17   18   19                                             
CONECT    2    1    3                                                       
CONECT    3    2    4   16                                                  
CONECT    4    3    5   20                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5   21                                                       
CONECT    7    5    8   15                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13   22   23                                             
CONECT   13   12   24                                                       
CONECT   14   11   15   25                                                  
CONECT   15   14   16    7                                                  
CONECT   16   15    3   26                                                  
CONECT   17    1                                                            
CONECT   18    1                                                            
CONECT   19    1                                                            
CONECT   20    4                                                            
CONECT   21    6                                                            
CONECT   22   12                                                            
CONECT   23   12                                                            
CONECT   24   13                                                            
CONECT   25   14                                                            
CONECT   26   16                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
8-Hydroxy-3-hydroxymethyl-6-methoxyisocoumarin	MeSH

Chemical Formula

C₁₁H₁₀O₅

Average Mass

222.1960 Da

Monoisotopic Mass

222.05282 Da

IUPAC Name

8-hydroxy-3-(hydroxymethyl)-6-methoxy-1H-isochromen-1-one

Traditional Name

8-hydroxy-3-(hydroxymethyl)-6-methoxyisochromen-1-one

CAS Registry Number

Not Available

SMILES

COC1=CC(O)=C2C(=O)OC(CO)=CC2=C1

InChI Identifier

InChI=1S/C11H10O5/c1-15-7-2-6-3-8(5-12)16-11(14)10(6)9(13)4-7/h2-4,12-13H,5H2,1H3

InChI Key

CAWNOJXNAUEIGB-UHFFFAOYSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces eurocidicus	NPAtlas	2272926

Species Where Detected

Species Name	Source	Reference
Streptomyces eurocidicus MI43-37F11	KNApSAcK Database	22123792

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as isocoumarins and derivatives. These are polycyclic compounds containing an isochromane which bears a ketone at the carbon C1.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isocoumarins and derivatives

Sub Class

Not Available

Direct Parent

Isocoumarins and derivatives

Alternative Parents

Substituents

Isocoumarin
Benzopyran
2-benzopyran
Anisole
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Pyranone
Pyran
Benzenoid
Vinylogous acid
Heteroaromatic compound
Lactone
Organoheterocyclic compound
Oxacycle
Ether
Alcohol
Primary alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Aromatic alcohol
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	1.28	ALOGPS
logP	1.4	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	9.47	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	57.29 m³·mol⁻¹	ChemAxon
Polarizability	21.41 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA020687

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00017060

Chemspider ID

4589088

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5486849

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kumagai H, Masuda T, Ohsono M, Hattori S, Naganawa H, Sawa T, Hamada M, Ishizuka M, Takeuchi T: Cytogenin, a novel antitumor substance. J Antibiot (Tokyo). 1990 Nov;43(11):1505-7. doi: 10.7164/antibiotics.43.1505. [PubMed:2272926 ]

Showing NP-Card for Cytogenin (NP0010916)

MOL for NP0010916 (Cytogenin)

3D MOL for NP0010916 (Cytogenin)

3D SDF for NP0010916 (Cytogenin)

3D-SDF for NP0010916 (Cytogenin)

PDB for NP0010916 (Cytogenin)

3D PDB for NP0010916 (Cytogenin)

SMILES for NP0010916 (Cytogenin)

INCHI for NP0010916 (Cytogenin)

Structure for NP0010916 (Cytogenin)

3D Structure for NP0010916 (Cytogenin)