NP-MRD: Showing NP-Card for [12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol (NP0164939)

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Record Information

Version

2.0

Created at

2022-09-02 23:55:30 UTC

Updated at

2022-09-02 23:55:30 UTC

NP-MRD ID

NP0164939

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol

Description

[12-(Hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]Tetradeca-1,3(8),9-trien-6-yl]methanol belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms. [12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol is found in Palythoa tuberculosa. [12-(Hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]Tetradeca-1,3(8),9-trien-6-yl]methanol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 36  0  0  0  0  0  0  0  0999 V2000
    4.1694    1.3104    1.8459 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8489   -0.0446    1.6596 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6932   -0.3480    0.1637 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6929    0.6172   -0.3782 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3067    0.1071   -0.2767 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2545    0.8630    0.0434 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9497    0.2846    0.1023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0939   -1.0617   -0.1627 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0424   -1.8273   -0.4848 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1541   -1.2576   -0.5444 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4144   -1.9748   -0.8873 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3833   -1.6709    0.0331 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4882   -1.5886   -0.0639 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4261   -0.7804   -0.6296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2643    0.5636   -0.4989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5895    1.1717   -0.0661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4445    2.5486    0.0734 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2016    1.0140    0.4469 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3893    1.8118    2.2054 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7276   -0.6410    1.9893 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9302   -0.2839    2.2188 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7175   -0.1559   -0.2672 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8304    1.5972    0.1183 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9061    0.7515   -1.4635 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7092   -1.7879   -1.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1921   -3.0608   -0.7994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7169   -1.8812    0.9920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4803   -2.5552   -0.6295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0371    0.9861   -1.5085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8507    0.7122    0.9135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4157    0.9098   -0.7583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7551    2.8378   -0.5617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4704    0.7399    1.4898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0933    2.0933    0.4030 H   0  0  0  0  0  0  0  0  0  0  0  0
 17 16  1  0
 16 15  1  0
 15 18  1  0
 18  7  1  0
  7  6  2  0
  6  5  1  0
  5 10  2  0
 10 11  1  0
 11 12  1  0
 12  3  1  0
  3  2  1  0
  2  1  1  0
  3  4  1  0
 10  9  1  0
  9  8  2  0
  8 13  1  0
 13 14  1  0
 14 15  1  0
  8  7  1  0
  4  5  1  0
 17 32  1  0
 16 30  1  0
 16 31  1  0
 15 29  1  6
 18 33  1  0
 18 34  1  0
 11 25  1  0
 11 26  1  0
  3 22  1  6
  2 20  1  0
  2 21  1  0
  1 19  1  0
  4 23  1  0
  4 24  1  0
 13 27  1  0
 13 28  1  0
M  END


  Mrv1533004201501462D          

 18 20  0  0  0  0            999 V2000
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  7 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  5 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  3 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0164939

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1CC2=NC3=C(COC(CO)C3)N=C2CO1

> <INCHI_IDENTIFIER>
InChI=1S/C12H16N2O4/c15-3-7-1-9-11(5-17-7)14-12-6-18-8(4-16)2-10(12)13-9/h7-8,15-16H,1-6H2

> <INCHI_KEY>
VAVQYCCDQASVOI-UHFFFAOYSA-N

> <FORMULA>
C12H16N2O4

> <MOLECULAR_WEIGHT>
252.27

> <EXACT_MASS>
252.111007003

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.627284992618673

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol

> <ALOGPS_LOGP>
-0.50

> <JCHEM_LOGP>
-1.6688478126666666

> <ALOGPS_LOGS>
-2.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.963299049057742

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.361239057729659

> <JCHEM_PKA_STRONGEST_BASIC>
0.24771503744885992

> <JCHEM_POLAR_SURFACE_AREA>
84.70000000000002

> <JCHEM_REFRACTIVITY>
61.2226

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.44e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.668  -2.310   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       6.668  -5.390   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   18                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   16                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    7   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15    5   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17    3                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₆N₂O₄

Average Mass

252.2700 Da

Monoisotopic Mass

252.11101 Da

IUPAC Name

[12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol

Traditional Name

[12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol

CAS Registry Number

Not Available

SMILES

OCC1CC2=NC3=C(COC(CO)C3)N=C2CO1

InChI Identifier

InChI=1S/C12H16N2O4/c15-3-7-1-9-11(5-17-7)14-12-6-18-8(4-16)2-10(12)13-9/h7-8,15-16H,1-6H2

InChI Key

VAVQYCCDQASVOI-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Palythoa tuberculosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrazines

Direct Parent

Pyrazines

Alternative Parents

Substituents

Pyrazine
Heteroaromatic compound
Oxacycle
Azacycle
Ether
Dialkyl ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
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	-0.5	ALOGPS
logP	-1.7	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	14.36	ChemAxon
pKa (Strongest Basic)	0.25	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	84.7 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	61.22 m³·mol⁻¹	ChemAxon
Polarizability	26.63 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

74051552

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol (NP0164939)

MOL for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

3D MOL for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

3D SDF for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

3D-SDF for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

PDB for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

3D PDB for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

SMILES for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

INCHI for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

Structure for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)

3D Structure for NP0164939 ([12-(hydroxymethyl)-5,13-dioxa-2,9-diazatricyclo[8.4.0.0³,⁸]tetradeca-1(10),2,8-trien-6-yl]methanol)