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Showing NP-Card for FAPy-adenine (NP0000043)

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Record Information
Version1.0
Created at2006-08-24 12:46:15 UTC
Updated at2021-06-30 02:06:03 UTC
NP-MRD IDNP0000043
Secondary Accession NumbersNone
Natural Product Identification
Common NameFAPy-adenine
DescriptionFapy-adenine is an oxidized DNA base. Oxidized nucleosides are biochemical markers for tumors, aging, and neurodegenerative diseases (PMID 15116424 ). Oxidative stress damage to DNA bases may contribute to neuronal loss in Alzheimer's disease (AD). Increased levels were observed in parietal, temporal, occipital, and frontal lobe, superior temporal gyrus, and hippocampus areas of the brain in patients with AD. (PMID 9109533 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000043 (FAPy-adenine)


  Mrv1652305271900122D          

 11 11  0  0  0  0            999 V2000
   13.5984   -5.6885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7109   -4.9741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9484   -5.6885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3609   -6.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3609   -4.9741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1859   -6.4031    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.1859   -4.9741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.1234   -5.6885    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8859   -4.9741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9484   -7.1175    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.9484   -4.2596    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  2  0  0  0  0
  1  6  1  0  0  0  0
  2  8  1  0  0  0  0
  2  9  2  0  0  0  0
  3  4  1  0  0  0  0
  3  8  1  0  0  0  0
  3  5  2  0  0  0  0
  4  6  2  0  0  0  0
  5  7  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
M  END
Download

3D MOL for NP0000043 (FAPy-adenine)

HMDB0004816
     RDKit          3D
FAPy-adenine
 18 18  0  0  0  0  0  0  0  0999 V2000
   -0.1477    2.1966   -0.8375 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4310    1.1605    0.0887 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1810    1.5354    1.1550 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5669    0.6756    2.0973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1942   -0.6024    1.9758 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4572   -1.0715    0.9670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0875   -2.4427    0.8859 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0548   -0.1494   -0.0235 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7590   -0.6229   -1.0532 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6844    0.0325   -1.8799 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9772    1.2227   -1.8407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4657    2.9924   -0.4907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5307    2.1856   -1.8103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1718    1.0043    2.9475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7640   -3.1748    1.1914 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8476   -2.6986    0.5250 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6252   -1.6946   -1.2372 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2276   -0.5485   -2.6605 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  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
  8  2  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  7 15  1  0
  7 16  1  0
  9 17  1  0
 10 18  1  0
M  END
Download

3D SDF for NP0000043 (FAPy-adenine)


  Mrv1652305271900122D          

 11 11  0  0  0  0            999 V2000
   13.5984   -5.6885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7109   -4.9741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9484   -5.6885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3609   -6.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3609   -4.9741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1859   -6.4031    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.1859   -4.9741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.1234   -5.6885    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8859   -4.9741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9484   -7.1175    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.9484   -4.2596    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  2  0  0  0  0
  1  6  1  0  0  0  0
  2  8  1  0  0  0  0
  2  9  2  0  0  0  0
  3  4  1  0  0  0  0
  3  8  1  0  0  0  0
  3  5  2  0  0  0  0
  4  6  2  0  0  0  0
  5  7  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000043

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC=NC(N)=C1NC=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H7N5O/c6-4-3(10-2-11)5(7)9-1-8-4/h1-2H,(H,10,11)(H4,6,7,8,9)

> <INCHI_KEY>
MVYUVUOSXNYQLL-UHFFFAOYSA-N

> <FORMULA>
C5H7N5O

> <MOLECULAR_WEIGHT>
153.142

> <EXACT_MASS>
153.065059871

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.85331815393523

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-(4,6-diaminopyrimidin-5-yl)formamide

> <ALOGPS_LOGP>
-1.36

> <JCHEM_LOGP>
-1.2301897326666666

> <ALOGPS_LOGS>
-1.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.929848073399503

> <JCHEM_PKA_STRONGEST_BASIC>
6.913103431709443

> <JCHEM_POLAR_SURFACE_AREA>
106.92

> <JCHEM_REFRACTIVITY>
43.122600000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.67e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-(4,6-diaminopyrimidin-5-yl)formamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000043 (FAPy-adenine)

HMDB0004816
     RDKit          3D
FAPy-adenine
 18 18  0  0  0  0  0  0  0  0999 V2000
   -0.1477    2.1966   -0.8375 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4310    1.1605    0.0887 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1810    1.5354    1.1550 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5669    0.6756    2.0973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1942   -0.6024    1.9758 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4572   -1.0715    0.9670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0875   -2.4427    0.8859 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0548   -0.1494   -0.0235 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7590   -0.6229   -1.0532 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6844    0.0325   -1.8799 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9772    1.2227   -1.8407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4657    2.9924   -0.4907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5307    2.1856   -1.8103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1718    1.0043    2.9475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7640   -3.1748    1.1914 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8476   -2.6986    0.5250 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6252   -1.6946   -1.2372 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2276   -0.5485   -2.6605 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  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
  8  2  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  7 15  1  0
  7 16  1  0
  9 17  1  0
 10 18  1  0
M  END
Download

PDB for NP0000043 (FAPy-adenine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      25.384 -10.619   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.994  -9.285   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      22.304 -10.619   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      23.074 -11.952   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      23.074  -9.285   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      24.614 -11.952   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      24.614  -9.285   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      20.764 -10.619   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      18.454  -9.285   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      22.304 -13.286   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0      22.304  -7.951   0.000  0.00  0.00           N+0
CONECT    1    7    6                                                       
CONECT    2    8    9                                                       
CONECT    3    4    8    5                                                  
CONECT    4    3    6   10                                                  
CONECT    5    3    7   11                                                  
CONECT    6    1    4                                                       
CONECT    7    1    5                                                       
CONECT    8    2    3                                                       
CONECT    9    2                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for NP0000043 (FAPy-adenine)

COMPND    HMDB0004816
HETATM    1  N1  UNL     1      -0.148   2.197  -0.838  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.431   1.161   0.089  1.00  0.00           C  
HETATM    3  N2  UNL     1      -1.181   1.535   1.155  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.567   0.676   2.097  1.00  0.00           C  
HETATM    5  N3  UNL     1      -1.194  -0.602   1.976  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.457  -1.072   0.967  1.00  0.00           C  
HETATM    7  N4  UNL     1      -0.088  -2.443   0.886  1.00  0.00           N  
HETATM    8  C4  UNL     1      -0.055  -0.149  -0.024  1.00  0.00           C  
HETATM    9  N5  UNL     1       0.759  -0.623  -1.053  1.00  0.00           N  
HETATM   10  C5  UNL     1       1.684   0.032  -1.880  1.00  0.00           C  
HETATM   11  O1  UNL     1       1.977   1.223  -1.841  1.00  0.00           O  
HETATM   12  H1  UNL     1       0.466   2.992  -0.491  1.00  0.00           H  
HETATM   13  H2  UNL     1      -0.531   2.186  -1.810  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.172   1.004   2.948  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.764  -3.175   1.191  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.848  -2.699   0.525  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.625  -1.695  -1.237  1.00  0.00           H  
HETATM   18  H7  UNL     1       2.228  -0.549  -2.661  1.00  0.00           H  
CONECT    1    2   12   13
CONECT    2    3    3    8
CONECT    3    4
CONECT    4    5    5   14
CONECT    5    6
CONECT    6    7    8    8
CONECT    7   15   16
CONECT    8    9
CONECT    9   10   17
CONECT   10   11   11   18
END
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SMILES for NP0000043 (FAPy-adenine)

NC1=NC=NC(N)=C1NC=O
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INCHI for NP0000043 (FAPy-adenine)

InChI=1S/C5H7N5O/c6-4-3(10-2-11)5(7)9-1-8-4/h1-2H,(H,10,11)(H4,6,7,8,9)
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View in JSmol
Synonyms
ValueSource
4,6-Diamino-5-(formylamino)pyrimidineChEBI
4,6-Diamino-5-N-formamidopyrimidineChEBI
4,6-Diamino-5-pyrimidinylformamideChEBI
FAPYChEBI
FapyadeChEBI
4,6-Diamino-5-formamidopyrimidineHMDB
N-(4,6-Diamino-5-pyrimidinyl)-formamideHMDB
N-(4,6-Diamino-5-pyrimidinyl)formamideHMDB
FAPy-adenineChEBI
Chemical FormulaC5H7N5O
Average Mass153.1420 Da
Monoisotopic Mass153.06506 Da
IUPAC NameN-(4,6-diaminopyrimidin-5-yl)formamide
Traditional NameN-(4,6-diaminopyrimidin-5-yl)formamide
CAS Registry Number5122-36-1
SMILES
NC1=NC=NC(N)=C1NC=O
InChI Identifier
InChI=1S/C5H7N5O/c6-4-3(10-2-11)5(7)9-1-8-4/h1-2H,(H,10,11)(H4,6,7,8,9)
InChI KeyMVYUVUOSXNYQLL-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)V.dorna832021-08-31View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)V.dorna832021-08-31View Spectrum
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)Varshavi.d262021-07-20View 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 aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentAminopyrimidines and derivatives
Alternative Parents
Substituents
  • Aminopyrimidine
  • Hydropyrimidine
  • Imidolactam
  • Heteroaromatic compound
  • Carboximidic acid
  • Carboximidic acid derivative
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Azacycle
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Amine
  • Organopnictogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point224 - 226 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility8.67 g/LALOGPS
logP-1.4ALOGPS
logP-1.2ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)11.93ChemAxon
pKa (Strongest Basic)6.91ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area106.92 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity43.12 m³·mol⁻¹ChemAxon
Polarizability13.85 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0004816
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023426
KNApSAcK IDNot Available
Chemspider ID102870
KEGG Compound IDC06502
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID7080
PubChem Compound114926
PDB IDNot Available
ChEBI ID27983
Good Scents IDNot Available
References
General References
  1. Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. [PubMed:15116424 ]
  2. Lyras L, Cairns NJ, Jenner A, Jenner P, Halliwell B: An assessment of oxidative damage to proteins, lipids, and DNA in brain from patients with Alzheimer's disease. J Neurochem. 1997 May;68(5):2061-9. [PubMed:9109533 ]
  3. Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T: Unexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions. Nat Chem Biol. 2013 Jul;9(7):455-61. doi: 10.1038/nchembio.1254. Epub 2013 May 19. [PubMed:23685671 ]
  4. Min K, Ebeler SE: Flavonoid effects on DNA oxidation at low concentrations relevant to physiological levels. Food Chem Toxicol. 2008 Jan;46(1):96-104. doi: 10.1016/j.fct.2007.07.002. Epub 2007 Jul 14. [PubMed:17707569 ]