NP-MRD: Showing NP-Card for dehydrocoformycin (NP0255597)

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Record Information

Version

2.0

Created at

2022-09-07 20:08:49 UTC

Updated at

2022-09-07 20:08:49 UTC

NP-MRD ID

NP0255597

Secondary Accession Numbers

None

Natural Product Identification

Common Name

dehydrocoformycin

Description

Dehydrocoformycin, also known as 8-oxocoformycin, belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). dehydrocoformycin is found in Apis cerana. Based on a literature review very few articles have been published on dehydrocoformycin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 36  0  0  0  0  0  0  0  0999 V2000
    4.0859   -0.2175    2.2766 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6354   -0.0511    1.1176 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5625    0.5802    0.1806 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9795    1.3382   -0.8635 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8957    1.3384   -1.5256 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8180    0.4306   -1.3600 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4490   -0.3017   -0.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2509   -0.5181    0.8937 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5716   -1.2514    1.7892 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3459   -1.4962    1.2543 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2886   -0.9147    0.0466 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8264   -0.9199   -0.8740 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1930    0.3832   -1.1071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3699    0.6444   -0.4542 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3229    1.9256    0.3535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3068    1.7885    1.2955 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6486   -0.4899    0.4896 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9789   -0.6962    0.7485 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0230   -1.6429   -0.3068 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8876   -2.0691   -1.3095 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2701   -0.2135   -0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2201    1.2772    0.7777 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7600    2.0913   -2.2919 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1981    0.2637   -2.1874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4141   -2.0706    1.7655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5496   -1.3897   -1.8383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2086    0.7734   -1.1865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0905    2.8037   -0.2784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2988    2.0583    0.8572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1999    2.5756    1.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0512   -0.3481    1.3867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5991   -0.2263    0.1674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7826   -2.4976    0.3145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5797   -2.9581   -1.6032 H   0  0  0  0  0  0  0  0  0  0  0  0
 16 15  1  0
 15 14  1  0
 14 13  1  0
 13 12  1  0
 12 19  1  0
 19 20  1  0
 19 17  1  0
 17 18  1  0
 12 11  1  0
 11 10  1  0
 10  9  2  0
  9  8  1  0
  8  7  2  0
  7  6  1  0
  6  5  1  0
  5  4  2  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
 17 14  1  0
  7 11  1  0
  2  8  1  0
 16 30  1  0
 15 28  1  0
 15 29  1  0
 14 27  1  6
 12 26  1  6
 19 33  1  1
 20 34  1  0
 17 31  1  1
 18 32  1  0
 10 25  1  0
  6 24  1  0
  5 23  1  0
  3 21  1  0
  3 22  1  0
M  END


  Mrv1652309072222082D          

 20 22  0  0  1  0            999 V2000
    3.1690    1.5257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3526    0.7214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1569    0.5378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5149   -0.2055    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1569   -0.9488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3526   -1.1324    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7076   -0.6180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7076    0.2070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230    0.4619    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4380   -0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230   -0.8729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6680   -1.6576    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1530   -2.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6680   -2.9924    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9230   -3.7771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7299   -3.9486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8834   -2.7375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2160   -3.2224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8834   -1.9125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2160   -1.4276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  7 11  1  0  0  0  0
 12 11  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  1  0  0  0
 17 19  1  0  0  0  0
 12 19  1  0  0  0  0
 19 20  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0255597

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1NC=NCC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N4O5/c16-2-6-8(18)9(19)11(20-6)15-4-14-7-5(17)1-12-3-13-10(7)15/h3-4,6,8-9,11,16,18-19H,1-2H2,(H,12,13)/t6-,8-,9-,11-/m1/s1

> <INCHI_KEY>
PICFAMQFTUCMDC-PNHWDRBUSA-N

> <FORMULA>
C11H14N4O5

> <MOLECULAR_WEIGHT>
282.256

> <EXACT_MASS>
282.096419567

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.529440211951112

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H,4H,7H,8H-imidazo[4,5-d][1,3]diazepin-8-one

> <JCHEM_LOGP>
-1.895708234666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.245070221203859

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.043464310549574

> <JCHEM_PKA_STRONGEST_BASIC>
5.462116962777623

> <JCHEM_POLAR_SURFACE_AREA>
129.20000000000002

> <JCHEM_REFRACTIVITY>
65.66040000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4H,7H-imidazo[4,5-d][1,3]diazepin-8-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       5.916   2.848   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.258   1.347   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.760   1.004   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       8.428  -0.384   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       7.760  -1.771   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.258  -2.114   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       5.054  -1.154   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.054   0.386   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.590   0.862   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       2.684  -0.384   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       3.590  -1.629   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       3.114  -3.094   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.019  -4.340   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.114  -5.586   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.590  -7.050   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.096  -7.371   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.649  -5.110   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.403  -6.015   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.649  -3.570   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.403  -2.665   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    2    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    7   12                                                  
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   12   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Value	Source
8-Oxocoformycin	ChEBI

Chemical Formula

C₁₁H₁₄N₄O₅

Average Mass

282.2560 Da

Monoisotopic Mass

282.09642 Da

IUPAC Name

3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H,4H,7H,8H-imidazo[4,5-d][1,3]diazepin-8-one

Traditional Name

3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4H,7H-imidazo[4,5-d][1,3]diazepin-8-one

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1NC=NCC2=O

InChI Identifier

InChI=1S/C11H14N4O5/c16-2-6-8(18)9(19)11(20-6)15-4-14-7-5(17)1-12-3-13-10(7)15/h3-4,6,8-9,11,16,18-19H,1-2H2,(H,12,13)/t6-,8-,9-,11-/m1/s1

InChI Key

PICFAMQFTUCMDC-PNHWDRBUSA-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
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

N-glycosyl compound
Imidazo-meta-diazepine
Imidazodiazepine
Pentose monosaccharide
Aryl alkyl ketone
Aryl ketone
Meta-diazepine
Monosaccharide
N-substituted imidazole
Azole
Heteroaromatic compound
Imidazole
Vinylogous amide
Tetrahydrofuran
Ketone
Secondary alcohol
Organic 1,3-dipolar compound
Organoheterocyclic compound
Azacycle
Oxacycle
Carboxylic acid amidine
Formamidine
Amidine
Propargyl-type 1,3-dipolar organic compound
Primary alcohol
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

coformycins (CHEBI:16299 )

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	-1.9	ChemAxon
pKa (Strongest Acidic)	9.04	ChemAxon
pKa (Strongest Basic)	5.46	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	129.2 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	65.66 m³·mol⁻¹	ChemAxon
Polarizability	26.53 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

388753

KEGG Compound ID

C02243

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439686

PDB ID

Not Available

ChEBI ID

16299

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for dehydrocoformycin (NP0255597)

MOL for NP0255597 (dehydrocoformycin)

3D MOL for NP0255597 (dehydrocoformycin)

3D SDF for NP0255597 (dehydrocoformycin)

3D-SDF for NP0255597 (dehydrocoformycin)

PDB for NP0255597 (dehydrocoformycin)

3D PDB for NP0255597 (dehydrocoformycin)

SMILES for NP0255597 (dehydrocoformycin)

INCHI for NP0255597 (dehydrocoformycin)

Structure for NP0255597 (dehydrocoformycin)

3D Structure for NP0255597 (dehydrocoformycin)