NP-MRD: Showing NP-Card for 8-oxodeoxycoformycin (NP0252764)

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Record Information

Version

2.0

Created at

2022-09-07 16:23:20 UTC

Updated at

2022-09-07 16:23:20 UTC

NP-MRD ID

NP0252764

Secondary Accession Numbers

None

Natural Product Identification

Common Name

8-oxodeoxycoformycin

Description

Dehydrodeoxycoformycin belongs to the class of organic compounds known as imidazodiazepines. These are organic compounds containing an imidazole ring fused to a diazepine ring. Imidazole is 5-membered ring consisting of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Diazepine is a 7-membered ring consisting of five carbon and two nitrogen atoms. 8-oxodeoxycoformycin is found in Apis cerana and Trypanosoma brucei. Based on a literature review very few articles have been published on dehydrodeoxycoformycin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 35  0  0  0  0  0  0  0  0999 V2000
    4.3894    1.6763    1.7008 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9171    0.9281    0.8066 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8986    0.2041    0.0194 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5088   -1.0270   -0.5318 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4247   -1.5958   -0.9106 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1376   -1.0160   -0.8529 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6905    0.0584   -0.0167 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4630    0.9181    0.7163 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6485    1.7740    1.3564 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3920    1.4359    1.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3972    0.3925    0.1779 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7413   -0.2901   -0.4338 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3114   -1.3350    0.4869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7705   -0.9989    0.6079 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5924   -2.0931    0.2914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9451    0.0927   -0.4043 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8581    1.1824    0.1538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9515    2.1970   -0.7741 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7199    0.6652   -0.6300 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2944    0.8714   -0.8016 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8034    0.0288    0.6716 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5023   -2.6001   -1.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4288   -1.4232   -1.5003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5272    1.9141    1.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4748   -0.6932   -1.4345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2059   -2.3393    0.0481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7964   -1.2402    1.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0368   -0.6192    1.6224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9463   -1.9994   -0.6359 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3594   -0.2457   -1.3587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5153    1.5222    1.1486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8599    0.7325    0.2825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2840    2.9224   -0.6191 H   0  0  0  0  0  0  0  0  0  0  0  0
 18 17  1  0
 17 16  1  0
 16 19  1  0
 19 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  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
 14 16  1  0
  7 11  1  0
  2  8  1  0
 18 33  1  0
 17 31  1  0
 17 32  1  0
 16 30  1  6
 12 25  1  6
 13 26  1  0
 13 27  1  0
 14 28  1  1
 15 29  1  0
 10 24  1  0
  6 23  1  0
  5 22  1  0
  3 20  1  0
  3 21  1  0
M  END


  Mrv1652309072218232D          

 19 21  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  1  0  0  0  0  0  0  0  0  0
    2.1530   -2.3250    0.0000 C   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 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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3022   -4.0429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8834   -1.9125    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  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 16 19  1  0  0  0  0
 12 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0252764

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N4O4/c16-3-8-6(17)1-9(19-8)15-5-14-10-7(18)2-12-4-13-11(10)15/h4-6,8-9,16-17H,1-3H2,(H,12,13)/t6-,8+,9+/m0/s1

> <INCHI_KEY>
PNAAOYLIDNSLKV-NBEYISGCSA-N

> <FORMULA>
C11H14N4O4

> <MOLECULAR_WEIGHT>
266.257

> <EXACT_MASS>
266.101504947

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.623242170090393

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-0.9950701716666661

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.637245206787128

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.046892437562853

> <JCHEM_PKA_STRONGEST_BASIC>
5.484024492351758

> <JCHEM_POLAR_SURFACE_AREA>
108.97000000000001

> <JCHEM_REFRACTIVITY>
64.1497

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
8-oxodeoxycoformycin

> <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  C   UNK     0       4.019  -4.340   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.114  -5.586   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.590  -7.050   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.649  -5.110   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.403  -6.015   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.564  -7.547   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.649  -3.570   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   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   12                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Value	Source
8-Oxodeoxycoformycin	ChEBI

Chemical Formula

C₁₁H₁₄N₄O₄

Average Mass

266.2570 Da

Monoisotopic Mass

266.10150 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C11H14N4O4/c16-3-8-6(17)1-9(19-8)15-5-14-10-7(18)2-12-4-13-11(10)15/h4-6,8-9,16-17H,1-3H2,(H,12,13)/t6-,8+,9+/m0/s1

InChI Key

PNAAOYLIDNSLKV-NBEYISGCSA-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
Trypanosoma brucei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as imidazodiazepines. These are organic compounds containing an imidazole ring fused to a diazepine ring. Imidazole is 5-membered ring consisting of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Diazepine is a 7-membered ring consisting of five carbon and two nitrogen atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazodiazepines

Sub Class

Not Available

Direct Parent

Imidazodiazepines

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

coformycins (CHEBI:27419 )

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

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

388906

KEGG Compound ID

C02957

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439866

PDB ID

Not Available

ChEBI ID

27419

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 8-oxodeoxycoformycin (NP0252764)

MOL for NP0252764 (8-oxodeoxycoformycin)

3D MOL for NP0252764 (8-oxodeoxycoformycin)

3D SDF for NP0252764 (8-oxodeoxycoformycin)

3D-SDF for NP0252764 (8-oxodeoxycoformycin)

PDB for NP0252764 (8-oxodeoxycoformycin)

3D PDB for NP0252764 (8-oxodeoxycoformycin)

SMILES for NP0252764 (8-oxodeoxycoformycin)

INCHI for NP0252764 (8-oxodeoxycoformycin)

Structure for NP0252764 (8-oxodeoxycoformycin)

3D Structure for NP0252764 (8-oxodeoxycoformycin)