NP-MRD: Showing NP-Card for coformycin (NP0269099)

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Record Information

Version

2.0

Created at

2022-09-08 14:25:46 UTC

Updated at

2022-09-08 14:25:47 UTC

NP-MRD ID

NP0269099

Secondary Accession Numbers

None

Natural Product Identification

Common Name

coformycin

Description

Coformycin 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). coformycin was first documented in 1981 (PMID: 7204504). Coformycin is a very strong basic compound (based on its pKa) (PMID: 11913523) (PMID: 14630012) (PMID: 6860359).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 38  0  0  0  0  0  0  0  0999 V2000
   -2.9405    2.5448    1.4021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3925    1.2249    1.4767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8151    0.4830    0.2947 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4197    0.4983    0.3086 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1251   -0.3476   -0.7501 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2648   -0.6316   -0.8921 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7768   -1.7392   -1.4529 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1381   -1.6474   -1.4044 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4793   -0.4862   -0.8151 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2867    0.1271   -0.5058 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1169    1.3878    0.1332 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9766    2.0129    0.8993 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2945    1.5655    1.2712 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9700    0.3224    0.9232 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8501    0.0240   -0.5545 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8240   -0.8645   -0.9302 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9303   -1.5807   -0.3997 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3607   -2.1630   -1.5833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1272   -0.9753    0.3078 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3147   -1.2751   -0.3882 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3059    2.7030    0.6784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1072    0.7854    2.4435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4952    1.2572    1.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1861    0.9954   -0.6159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5755    0.1130   -1.6602 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2281   -2.5692   -1.8746 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6910    2.9685    1.3090 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8140    2.2422    1.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6846   -0.5175    1.5657 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0676    0.5031    1.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9572    1.0201   -1.0729 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0616   -0.7330   -1.9005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3664   -2.2741    0.2500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5888   -1.4267   -2.2038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2159   -1.3141    1.3580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2150   -2.2335   -0.6543 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 19  3  1  0
 10  6  1  0
 15  9  1  0
  1 21  1  0
  2 22  1  0
  2 23  1  0
  3 24  1  6
  5 25  1  6
 17 33  1  1
 18 34  1  0
 19 35  1  1
 20 36  1  0
  7 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 14 30  1  0
 15 31  1  6
 16 32  1  0
M  END

 
  Mrv0541 07171215512D          
 
 20 22  0  0  1  0            999 V2000
   14.5262   -9.6004    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.7490   -9.3426    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2191  -10.6885    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.0115   -8.9522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7604   -8.5238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0969   -9.8506    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.5557  -10.2069    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9689  -11.4770    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.5451   -8.2811    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.1273   -8.0006    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2970   -9.6535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8847  -10.6885    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.1386  -11.4770    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.4542  -12.1442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3236   -8.1636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4119   -7.1169    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9559   -8.9067    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.0999  -10.4307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6534  -12.1442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.4858  -10.9804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  1  1  1  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  6 11  2  0  0  0  0
  7 12  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  1  6  0  0  0
 10 15  1  0  0  0  0
 10 16  1  1  0  0  0
 11 17  1  0  0  0  0
 12 18  1  1  0  0  0
 13 19  1  6  0  0  0
 18 20  1  0  0  0  0
  5  9  1  0  0  0  0
 12 13  1  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0269099

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CNC[C@H]2O

> <INCHI_IDENTIFIER>
InChI=1S/C11H16N4O5/c16-2-6-8(18)9(19)11(20-6)15-4-14-7-5(17)1-12-3-13-10(7)15/h3-6,8-9,11,16-19H,1-2H2,(H,12,13)/t5-,6-,8-,9-,11-/m1/s1

> <INCHI_KEY>
YOOVTUPUBVHMPG-LODYRLCVSA-N

> <FORMULA>
C11H16N4O5

> <MOLECULAR_WEIGHT>
284.2685

> <EXACT_MASS>
284.112069642

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
27.327430436886182

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-[(8R)-8-hydroxy-3H,6H,7H,8H-imidazo[4,5-d][1,3]diazepin-3-yl]-5-(hydroxymethyl)oxolane-3,4-diol

> <ALOGPS_LOGP>
-2.23

> <JCHEM_LOGP>
-2.917029090999999

> <ALOGPS_LOGS>
-1.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.145568188742288

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.371153016037677

> <JCHEM_PKA_STRONGEST_BASIC>
8.298245796822236

> <JCHEM_POLAR_SURFACE_AREA>
132.36

> <JCHEM_REFRACTIVITY>
66.4921

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.44e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
coformycin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUL-12         0                                  
HETATM    1  N   UNK     0      27.116 -17.921   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      25.665 -17.440   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      26.542 -19.952   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      28.021 -16.711   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      25.686 -15.911   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      24.448 -18.388   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      25.304 -19.053   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      26.075 -21.424   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      27.151 -15.458   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      24.504 -14.934   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      22.954 -18.020   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.051 -19.952   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.525 -21.424   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      26.981 -22.669   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      23.004 -15.239   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      25.035 -13.285   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0      22.318 -16.626   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      22.586 -19.471   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      23.620 -22.669   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      21.440 -20.497   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10    9                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12                                                       
CONECT    8    3   13   14                                                  
CONECT    9    4    5                                                       
CONECT   10    5   15   16                                                  
CONECT   11    6   17                                                       
CONECT   12    7   18   13                                                  
CONECT   13    8   19   12                                                  
CONECT   14    8                                                            
CONECT   15   10   17                                                       
CONECT   16   10                                                            
CONECT   17   11   15                                                       
CONECT   18   12   20                                                       
CONECT   19   13                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Value	Source
(R)-3,4,7,8-Tetrahydro-3-beta-D-ribofuranosylimidazo(4,5-D)(1,3)diazepin-8-ol	ChEBI
(R)-3,4,7,8-Tetrahydro-3-b-D-ribofuranosylimidazo(4,5-D)(1,3)diazepin-8-ol	Generator
(R)-3,4,7,8-Tetrahydro-3-β-D-ribofuranosylimidazo(4,5-D)(1,3)diazepin-8-ol	Generator

Chemical Formula

C₁₁H₁₆N₄O₅

Average Mass

284.2685 Da

Monoisotopic Mass

284.11207 Da

IUPAC Name

(2R,3R,4S,5R)-2-[(8R)-8-hydroxy-3H,6H,7H,8H-imidazo[4,5-d][1,3]diazepin-3-yl]-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

coformycin

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CNC[C@H]2O

InChI Identifier

InChI=1S/C11H16N4O5/c16-2-6-8(18)9(19)11(20-6)15-4-14-7-5(17)1-12-3-13-10(7)15/h3-6,8-9,11,16-19H,1-2H2,(H,12,13)/t5-,6-,8-,9-,11-/m1/s1

InChI Key

YOOVTUPUBVHMPG-LODYRLCVSA-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

Not Available

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
Meta-diazepine
Monosaccharide
N-substituted imidazole
Azole
Heteroaromatic compound
Imidazole
Tetrahydrofuran
Secondary alcohol
Amidine
Azacycle
Oxacycle
Carboxylic acid amidine
Formamidine
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Primary alcohol
Organonitrogen compound
Hydrocarbon derivative
Alcohol
Organopnictogen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

coformycins (CHEBI:16213 )

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	-2.2	ALOGPS
logP	-2.9	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	12.37	ChemAxon
pKa (Strongest Basic)	8.3	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	132.36 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	66.49 m³·mol⁻¹	ChemAxon
Polarizability	27.33 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

C01677

BioCyc ID

COFORMYCIN

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25447

PDB ID

Not Available

ChEBI ID

16213

Good Scents ID

Not Available

References

General References

Fujimori H, Yasuda M, Pan-Hou H: Enhancement of cellular adenosine triphosphate levels in PC12 cells by extracellular adenosine. Biol Pharm Bull. 2002 Mar;25(3):307-11. doi: 10.1248/bpb.25.307. [PubMed:11913523 ]
Okada T, Mochizuki T, Huang ZL, Eguchi N, Sugita Y, Urade Y, Hayaishi O: Dominant localization of adenosine deaminase in leptomeninges and involvement of the enzyme in sleep. Biochem Biophys Res Commun. 2003 Dec 5;312(1):29-34. doi: 10.1016/j.bbrc.2003.09.220. [PubMed:14630012 ]
Lukey T, Snyder FF: S-adenosylhomocysteine hydrolase activity, deoxyadenosine triphosphate accumulation, and competence of thymocyte and spleen leucocyte response to mitogens in coformycin-treated mice. Biochem Pharmacol. 1983 Apr 15;32(8):1399-406. doi: 10.1016/0006-2952(83)90453-7. [PubMed:6860359 ]
Debatisse M, Berry M, Buttin G: The potentiation of adenine toxicity to Chinese hamster cells by coformycin: suppression in mutants with altered regulation of purine biosynthesis or increased adenylate-deaminase activity. J Cell Physiol. 1981 Jan;106(1):1-11. doi: 10.1002/jcp.1041060102. [PubMed:7204504 ]
LOTUS database [Link]

Showing NP-Card for coformycin (NP0269099)

MOL for NP0269099 (coformycin)

3D MOL for NP0269099 (coformycin)

3D SDF for NP0269099 (coformycin)

3D-SDF for NP0269099 (coformycin)

PDB for NP0269099 (coformycin)

3D PDB for NP0269099 (coformycin)

SMILES for NP0269099 (coformycin)

INCHI for NP0269099 (coformycin)

Structure for NP0269099 (coformycin)

3D Structure for NP0269099 (coformycin)