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Showing NP-Card for 1-Methyladenine (NP0000865)

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Record Information
Version1.0
Created at2009-01-29 12:09:56 UTC
Updated at2020-11-24 22:18:58 UTC
NP-MRD IDNP0000865
Secondary Accession NumbersNone
Natural Product Identification
Common Name1-Methyladenine
Description1-Methyladenine is the product of reaction between 1-methyladenosine and water which is catalyzed by 1-methyladenosine nucleosidase (EC:3.2.2.13). 1-Methyladenine is a product of alkylation damage in DNA which can be repaired by damage reversal by oxidative demethylation, a reaction requiring ferrous iron and 2-oxoglutarate as cofactor and co-substrate, respectively (PMID:15576352 ). 1-Methyladenine is found to be associated with adenosine deaminase (ADA) deficiency, which is an inborn error of metabolism.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000865 (1-Methyladenine)


  Mrv1652305261923512D          

 11 12  0  0  0  0            999 V2000
   11.2805   -8.0761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2805   -8.9011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5660   -7.6636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5660   -9.3136    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8515   -8.0761    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8515   -8.9011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0650   -7.8212    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.5499   -8.4886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0649   -9.1560    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.5659   -6.8386    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.1370   -7.6636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  2  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  8  1  0  0  0  0
  9  2  2  0  0  0  0
 10  3  1  0  0  0  0
 11  5  1  0  0  0  0
M  END
Download

3D MOL for NP0000865 (1-Methyladenine)

HMDB0011599
     RDKit          3D
1-Methyladenine
 18 19  0  0  0  0  0  0  0  0999 V2000
   -2.4825    0.1532   -0.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0840    0.4364    0.1046 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7224    1.5498    0.7681 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5733    1.7701    1.0559 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5633    0.9279    0.7156 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8955    0.8869    0.8632 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3498   -0.2452    0.2936 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3233   -0.9536   -0.2304 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1872   -0.2835   -0.0041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1514   -0.4647   -0.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5194   -1.6401   -0.9744 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0940    1.0596   -0.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8816   -0.6645    0.4113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5491   -0.1200   -1.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5068    2.2443    1.0528 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3946   -0.5335    0.2674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9388   -2.4438   -0.4730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3571   -1.6792   -2.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10  2  1  0
  9  5  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  7 16  1  0
 11 17  1  0
 11 18  1  0
M  END
Download

3D SDF for NP0000865 (1-Methyladenine)


  Mrv1652305261923512D          

 11 12  0  0  0  0            999 V2000
   11.2805   -8.0761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2805   -8.9011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5660   -7.6636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5660   -9.3136    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8515   -8.0761    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8515   -8.9011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0650   -7.8212    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.5499   -8.4886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0649   -9.1560    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.5659   -6.8386    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.1370   -7.6636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  2  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  8  1  0  0  0  0
  9  2  2  0  0  0  0
 10  3  1  0  0  0  0
 11  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000865

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=NC2=NC=NC2=C1N

> <INCHI_IDENTIFIER>
InChI=1S/C6H7N5/c1-11-3-10-6-4(5(11)7)8-2-9-6/h2-3H,7H2,1H3

> <INCHI_KEY>
HPZMWTNATZPBIH-UHFFFAOYSA-N

> <FORMULA>
C6H7N5

> <MOLECULAR_WEIGHT>
149.1533

> <EXACT_MASS>
149.070145249

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.426283428034452

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methyl-1H-purin-6-amine

> <ALOGPS_LOGP>
-1.15

> <JCHEM_LOGP>
-0.4985114843333334

> <ALOGPS_LOGS>
-1.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
0.24199938140795818

> <JCHEM_POLAR_SURFACE_AREA>
69.62

> <JCHEM_REFRACTIVITY>
41.8065

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.91e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-methyl-1H-purin-6-amine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000865 (1-Methyladenine)

HMDB0011599
     RDKit          3D
1-Methyladenine
 18 19  0  0  0  0  0  0  0  0999 V2000
   -2.4825    0.1532   -0.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0840    0.4364    0.1046 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7224    1.5498    0.7681 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5733    1.7701    1.0559 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5633    0.9279    0.7156 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8955    0.8869    0.8632 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3498   -0.2452    0.2936 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3233   -0.9536   -0.2304 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1872   -0.2835   -0.0041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1514   -0.4647   -0.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5194   -1.6401   -0.9744 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0940    1.0596   -0.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8816   -0.6645    0.4113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5491   -0.1200   -1.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5068    2.2443    1.0528 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3946   -0.5335    0.2674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9388   -2.4438   -0.4730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3571   -1.6792   -2.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10  2  1  0
  9  5  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  7 16  1  0
 11 17  1  0
 11 18  1  0
M  END
Download

PDB for NP0000865 (1-Methyladenine)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0      21.057 -15.075   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.057 -16.615   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      19.723 -14.305   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      19.723 -17.385   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      18.389 -15.075   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      18.389 -16.615   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      22.521 -14.600   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      23.426 -15.845   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      22.521 -17.091   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      19.723 -12.765   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      17.056 -14.305   0.000  0.00  0.00           C+0
CONECT    1    3    7    2                                                  
CONECT    2    4    1    9                                                  
CONECT    3    1    5   10                                                  
CONECT    4    2    6                                                       
CONECT    5    3    6   11                                                  
CONECT    6    4    5                                                       
CONECT    7    1    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    2                                                       
CONECT   10    3                                                            
CONECT   11    5                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for NP0000865 (1-Methyladenine)

COMPND    HMDB0011599
HETATM    1  C1  UNL     1      -2.482   0.153  -0.231  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.084   0.436   0.105  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.722   1.550   0.768  1.00  0.00           C  
HETATM    4  N2  UNL     1       0.573   1.770   1.056  1.00  0.00           N  
HETATM    5  C3  UNL     1       1.563   0.928   0.716  1.00  0.00           C  
HETATM    6  N3  UNL     1       2.896   0.887   0.863  1.00  0.00           N  
HETATM    7  C4  UNL     1       3.350  -0.245   0.294  1.00  0.00           C  
HETATM    8  N4  UNL     1       2.323  -0.954  -0.230  1.00  0.00           N  
HETATM    9  C5  UNL     1       1.187  -0.284  -0.004  1.00  0.00           C  
HETATM   10  C6  UNL     1      -0.151  -0.465  -0.276  1.00  0.00           C  
HETATM   11  N5  UNL     1      -0.519  -1.640  -0.974  1.00  0.00           N  
HETATM   12  H1  UNL     1      -3.094   1.060  -0.022  1.00  0.00           H  
HETATM   13  H2  UNL     1      -2.882  -0.665   0.411  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.549  -0.120  -1.305  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.507   2.244   1.053  1.00  0.00           H  
HETATM   16  H5  UNL     1       4.395  -0.534   0.267  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.939  -2.444  -0.473  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.357  -1.679  -2.017  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3   10
CONECT    3    4    4   15
CONECT    4    5
CONECT    5    6    6    9
CONECT    6    7
CONECT    7    8    8   16
CONECT    8    9
CONECT    9   10   10
CONECT   10   11
CONECT   11   17   18
END
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SMILES for NP0000865 (1-Methyladenine)

CN1C=NC2=NC=NC2=C1N
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INCHI for NP0000865 (1-Methyladenine)

InChI=1S/C6H7N5/c1-11-3-10-6-4(5(11)7)8-2-9-6/h2-3H,7H2,1H3
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View in JSmol
Synonyms
ValueSource
N1-MethyladenineChEBI
1, 9-Dihydro-1-methyl-6H-purin-6-imineHMDB
1-Methyl-1H-purin-6-amineHMDB
1-Methyl-1H-purin-6-ylamineHMDB
1-Methyl-adenineHMDB
Chemical FormulaC6H7N5
Average Mass149.1533 Da
Monoisotopic Mass149.07015 Da
IUPAC Name1-methyl-1H-purin-6-amine
Traditional Name1-methyl-1H-purin-6-amine
CAS Registry Number5142-22-3
SMILES
CN1C=NC2=NC=NC2=C1N
InChI Identifier
InChI=1S/C6H7N5/c1-11-3-10-6-4(5(11)7)8-2-9-6/h2-3H,7H2,1H3
InChI KeyHPZMWTNATZPBIH-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)V.dorna832021-08-09View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 6-aminopurines. These are purines that carry an amino group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassImidazopyrimidines
Sub ClassPurines and purine derivatives
Direct Parent6-aminopurines
Alternative Parents
Substituents
  • 6-aminopurine
  • Aminopyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Organonitrogen compound
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility1.91 g/LALOGPS
logP-1.2ALOGPS
logP-0.5ChemAxon
logS-1.9ALOGPS
pKa (Strongest Basic)0.24ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area69.62 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity41.81 m³·mol⁻¹ChemAxon
Polarizability14.43 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0011599
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028310
KNApSAcK IDNot Available
Chemspider ID71157
KEGG Compound IDC02216
BioCyc ID1-METHYLADENINE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound78821
PDB IDNot Available
ChEBI ID18083
Good Scents IDNot Available
References
General References
  1. Falnes PO: Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins. Nucleic Acids Res. 2004 Dec 1;32(21):6260-7. Print 2004. [PubMed:15576352 ]
  2. Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225 ]
  3. Nakano T, Kontani K, Kurosu H, Katada T, Hoshi M, Chiba K: G-protein betagamma subunit-dependent phosphorylation of 62-kDa protein in the early signaling pathway of starfish oocyte maturation induced by 1-methyladenine. Dev Biol. 1999 May 1;209(1):200-9. doi: 10.1006/dbio.1999.9248. [PubMed:10208753 ]
  4. Leiros I, Nabong MP, Grosvik K, Ringvoll J, Haugland GT, Uldal L, Reite K, Olsbu IK, Knaevelsrud I, Moe E, Andersen OA, Birkeland NK, Ruoff P, Klungland A, Bjelland S: Structural basis for enzymatic excision of N1-methyladenine and N3-methylcytosine from DNA. EMBO J. 2007 Apr 18;26(8):2206-17. doi: 10.1038/sj.emboj.7601662. Epub 2007 Mar 29. [PubMed:17396151 ]
  5. Banys K, Giebultowicz J, Sobczak M, Wyrebiak R, Bielecki W, Wrzesien R, Bobrowska-Korczak B: Effect of Genistein Supplementation on the Progression of Neoplasms and the Level of the Modified Nucleosides in Rats With Mammary Cancer. In Vivo. 2021 Jul-Aug;35(4):2059-2072. doi: 10.21873/invivo.12475. [PubMed:34182481 ]
  6. Wan L, Lam SL, Lee HK, Guo P: Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell. Int J Mol Sci. 2021 Mar 31;22(7). pii: ijms22073633. doi: 10.3390/ijms22073633. [PubMed:33807305 ]
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