NP-MRD: Showing NP-Card for ganciclovir (NP0242789)

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Record Information

Version

2.0

Created at

2022-09-07 03:11:24 UTC

Updated at

2022-09-07 03:11:24 UTC

NP-MRD ID

NP0242789

Secondary Accession Numbers

None

Natural Product Identification

Common Name

ganciclovir

Description

Ganciclovir, also known as GA2 or cytovene, belongs to the class of organic compounds known as hypoxanthines. Hypoxanthines are compounds containing the purine derivative 1H-purin-6(9H)-one. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring. Ganciclovir is a drug which is used for induction and maintenance in the treatment of cytomegalovirus (cmv) retinitis in immunocompromised patients, including patients with acquired immunodeficiency syndrome (aids). Also used in the treatment of severe cytomegalovirus (cmv) disease, including cmv pneumonia, cmv gastrointestinal disease, and disseminated cmv infections, in immunocompromised patients. Ganciclovir is a moderately basic compound (based on its pKa). ganciclovir is found in Homo sapiens. ganciclovir was first documented in 1999 (PMID: 10197958). An oxopurine that is guanine substituted by a methyl group at position 9.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 32  0  0  0  0  0  0  0  0999 V2000
    3.9586   -1.6519   -1.5696 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3514   -0.6062   -0.8262 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1767   -0.8544   -0.2182 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5521    0.1040    0.5037 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1188    1.3455    0.6205 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    2.0796    1.3790 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2345    1.3432    1.7407 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3906    0.1293    1.2037 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4946   -1.0024    1.3314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4321   -1.1177    0.3438 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3214   -0.0895    0.1950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1931    0.4568   -1.2357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4923   -0.6108   -2.0802 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7590   -0.6290    0.2610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6413    0.4428    0.1064 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3310    1.6054   -0.0056 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8217    2.7570    0.1235 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9094    0.6194   -0.7101 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6654   -2.2426   -1.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6824   -1.7954   -2.5604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6005    1.6829    2.3684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9677   -0.9917    2.3491 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1264   -1.9260    1.3102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1888    0.7436    0.9081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9853    1.2172   -1.3662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1807    0.8497   -1.4243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1088   -1.4230   -1.6553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8624   -1.1457    1.2146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9213   -1.3122   -0.5959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2837    1.2278    0.5656 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8189    0.7944   -1.1871 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
  5 16  1  0
 16 17  2  0
 16 18  1  0
 18  2  1  0
  8  4  1  0
  1 19  1  0
  1 20  1  0
  7 21  1  0
  9 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
 18 31  1  0
M  END


  Mrv0541 04111413432D          

 18 19  0  0  0  0            999 V2000
    2.8150   -1.0862    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0808   -0.8042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0681    0.0205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8613    0.2481    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3228   -0.4359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2699   -1.1917    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6113   -0.7547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6399    0.0699    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3683    0.4575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3553    1.2726    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1230   -1.1451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8150   -1.9111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5216   -2.3189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2368   -1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9311   -2.3065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2370   -1.0692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9364   -0.6655    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6356   -1.8995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  2  0  0  0  0
  7 11  1  0  0  0  0
  1 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0242789

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC2=C(N=CN2COC(CO)CO)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N5O4/c10-9-12-7-6(8(17)13-9)11-3-14(7)4-18-5(1-15)2-16/h3,5,15-16H,1-2,4H2,(H3,10,12,13,17)

> <INCHI_KEY>
IRSCQMHQWWYFCW-UHFFFAOYSA-N

> <FORMULA>
C9H13N5O4

> <MOLECULAR_WEIGHT>
255.2306

> <EXACT_MASS>
255.096753929

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
24.154164573887854

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-9-{[(1,3-dihydroxypropan-2-yl)oxy]methyl}-6,9-dihydro-1H-purin-6-one

> <ALOGPS_LOGP>
-1.83

> <JCHEM_LOGP>
-2.179902508666667

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.298583858244307

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.159807017663518

> <JCHEM_PKA_STRONGEST_BASIC>
1.7601277428844484

> <JCHEM_POLAR_SURFACE_AREA>
134.99

> <JCHEM_REFRACTIVITY>
61.029300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.15e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gancyclovir

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-APR-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-APR-14         0                                  
HETATM    1  N   UNK     0       5.255  -2.028   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.884  -1.501   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.860   0.038   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       5.341   0.463   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       6.203  -0.814   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.370  -2.225   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       1.141  -1.409   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       1.194   0.130   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       2.554   0.854   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.530   2.376   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0      -0.230  -2.138   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       5.255  -3.567   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.574  -4.329   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       7.909  -3.557   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.205  -4.305   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.909  -1.996   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.215  -1.242   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      10.520  -3.546   0.000  0.00  0.00           O+0
CONECT    1    2    5   12                                                  
CONECT    2    1    3    6                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    2    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8    3   10                                                  
CONECT   10    9                                                            
CONECT   11    7                                                            
CONECT   12    1   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14   18                                                       
CONECT   16   14   17                                                       
CONECT   17   16                                                            
CONECT   18   15                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
2-(6-Amino-purin-9-ylmethoxy)-propane-1,3-diol	ChEBI
2-Amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-1H-purin-6(9H)-one	ChEBI
2-Amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-3H-purin-6(9H)-one	ChEBI
2-Amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-9H-purin-6-ol	ChEBI
2-Amino-9-(2-hydroxy-1-hydroxymethyl-ethoxymethyl)-1,9-dihydro-purin-6-one	ChEBI
2-Amino-9-(2-hydroxy-1-hydroxymethylethoxymethyl)-6,9-dihydro-1H-6-purinone	ChEBI
9-((2-Hydroxy-1-(hydroxymethyl)ethoxy)methyl)guanine	ChEBI
9-(1,3-DIHYDROXY-propoxymethane)guanine	ChEBI
9-[(1,3-Dihydroxy-2-propoxy)methyl]guanine	ChEBI
GA2	ChEBI
Ganciclovirum	ChEBI
Gancyclovir	ChEBI
Cytovene	Kegg
Vitrasert	Kegg
Zirgan	Kegg
Ganciclovir sodium	HMDB
BIOLF-62	HMDB
Ganciclovir, monosodium salt	HMDB

Chemical Formula

C₉H₁₃N₅O₄

Average Mass

255.2306 Da

Monoisotopic Mass

255.09675 Da

IUPAC Name

2-amino-9-{[(1,3-dihydroxypropan-2-yl)oxy]methyl}-6,9-dihydro-1H-purin-6-one

Traditional Name

gancyclovir

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(N=CN2COC(CO)CO)C(=O)N1

InChI Identifier

InChI=1S/C9H13N5O4/c10-9-12-7-6(8(17)13-9)11-3-14(7)4-18-5(1-15)2-16/h3,5,15-16H,1-2,4H2,(H3,10,12,13,17)

InChI Key

IRSCQMHQWWYFCW-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
Homo sapiens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hypoxanthines. Hypoxanthines are compounds containing the purine derivative 1H-purin-6(9H)-one. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

Hypoxanthines

Alternative Parents

Substituents

6-oxopurine
Hypoxanthine
Aminopyrimidine
Pyrimidone
Glycerolipid
N-substituted imidazole
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Vinylogous amide
Azacycle
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxide
Alcohol
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Amine
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

oxopurine (CHEBI:465284 )
2-aminopurines (CHEBI:465284 )

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	-1.8	ALOGPS
logP	-2.2	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	10.16	ChemAxon
pKa (Strongest Basic)	1.76	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	134.99 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	61.03 m³·mol⁻¹	ChemAxon
Polarizability	24.15 Å³	ChemAxon
Number of Rings	2	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

HMDB0015139

DrugBank ID

DB01004

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

3336

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Ganciclovir

METLIN ID

Not Available

PubChem Compound

3454

PDB ID

Not Available

ChEBI ID

465284

Good Scents ID

Not Available

References

General References

Martinez A, Esteban AI, Castro A, Gil C, Conde S, Andrei G, Snoeck R, Balzarini J, De Clercq E: Novel potential agents for human cytomegalovirus infection: synthesis and antiviral activity evaluation of benzothiadiazine dioxide acyclonucleosides. J Med Chem. 1999 Apr 8;42(7):1145-50. doi: 10.1021/jm980327z. [PubMed:10197958 ]
LOTUS database [Link]

Showing NP-Card for ganciclovir (NP0242789)

MOL for NP0242789 (ganciclovir)

3D MOL for NP0242789 (ganciclovir)

3D SDF for NP0242789 (ganciclovir)

3D-SDF for NP0242789 (ganciclovir)

PDB for NP0242789 (ganciclovir)

3D PDB for NP0242789 (ganciclovir)

SMILES for NP0242789 (ganciclovir)

INCHI for NP0242789 (ganciclovir)

Structure for NP0242789 (ganciclovir)

3D Structure for NP0242789 (ganciclovir)