Showing metabocard for Nitrate (MMDBc0000221)

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Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:40:17 UTC
Update Date2024-09-29 15:23:35 UTC
Metabolite IDMMDBc0000221
Metabolite Identification
Common NameNitrate
DescriptionIn inorganic chemistry, a nitrate is a salt of nitric acid. In organic chemistry the esters of nitric acid and various alcohols are called nitrates. The nitrate ion is a polyatomic anion with the empirical formula NO3- and a molecular mass of 62.01 daltons; it consists of one central nitrogen atom surrounded by three identical oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a negative one formal charge. Nitrates should not be confused with nitrites, the salts of nitrous acid. Organic compounds containing the nitro functional group (which has the same formula and structure as the nitrate ion save that one of the O2 atoms is replaced by the R group) are known as nitro compounds. Nitrate ions can be toxic. In particular, nitrate toxicosis in humans occurs through enterohepatic metabolism of nitrates to ammonia, with nitrite being an intermediate. Nitrites oxidize the iron atoms in hemoglobin from Ferrous Iron (2+) to Ferric Iron (3+), rendering it unable to carry oxygen. This condition is called methemoglobinemia and can lead to a lack of oxygen in tissues. Methemoglobinemia can be treated with methylene blue. -- Wikipedia .
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000556b6ae80d98>


  Mrv1652306222023342D          

  4  3  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  1  2  0  0  0  0
M  CHG  1   2  -1
M  END
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3D MOL for #<Metabolite:0x0000556b6ae80d98>

HMDB0002878
     RDKit          3D
Nitrate
  4  3  0  0  0  0  0  0  0  0999 V2000
   -0.5467    1.1635    0.0060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0091    0.0296    0.0001 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.7880   -1.0875    0.0058 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3438   -0.1057   -0.0120 O   0  0  0  0  0  1  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
M  CHG  3   2   1   3  -1   4  -1
M  END
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3D SDF for #<Metabolite:0x0000556b6ae80d98>


  Mrv1652306222023342D          

  4  3  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  1  2  0  0  0  0
M  CHG  1   2  -1
M  END
> <DATABASE_ID>
MMDBc0000221

> <DATABASE_NAME>
MIME

> <SMILES>
[O-]N(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/NO3/c2-1(3)4/q-1

> <INCHI_KEY>
NHNBFGGVMKEFGY-UHFFFAOYSA-N

> <FORMULA>
NO3

> <MOLECULAR_WEIGHT>
62.0049

> <EXACT_MASS>
61.987817871

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
3.275441232355817

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
nitrate

> <JCHEM_LOGP>
0.8368003898615884

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_BASIC>
-9.93762264919614

> <JCHEM_POLAR_SURFACE_AREA>
66.2

> <JCHEM_REFRACTIVITY>
8.347100000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
nitrate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000556b6ae80d98>

HMDB0002878
     RDKit          3D
Nitrate
  4  3  0  0  0  0  0  0  0  0999 V2000
   -0.5467    1.1635    0.0060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0091    0.0296    0.0001 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.7880   -1.0875    0.0058 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3438   -0.1057   -0.0120 O   0  0  0  0  0  1  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
M  CHG  3   2   1   3  -1   4  -1
M  END
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PDB for #<Metabolite:0x0000556b6ae80d98>

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  N   UNK     0       1.540   0.000   0.000  0.00  0.00           N+0
HETATM    2  O   UNK     0       2.310   1.334   0.000  0.00  0.00           O-1
HETATM    3  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for #<Metabolite:0x0000556b6ae80d98>

COMPND    HMDB0002878
HETATM    1  O1  UNL     1      -0.547   1.163   0.006  1.00  0.00           O  
HETATM    2  N1  UNL     1      -0.009   0.030   0.000  1.00  0.00           N1+
HETATM    3  O2  UNL     1      -0.788  -1.087   0.006  1.00  0.00           O1-
HETATM    4  O3  UNL     1       1.344  -0.106  -0.012  1.00  0.00           O1-
CONECT    1    2    2
CONECT    2    3    4
END
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SMILES for #<Metabolite:0x0000556b6ae80d98>

[O-]N(=O)=O
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INCHI for #<Metabolite:0x0000556b6ae80d98>

InChI=1S/NO3/c2-1(3)4/q-1
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Synonyms
ValueSource
[NO3](-)ChEBI
NITRATE ionChEBI
Nitrate(1-)ChEBI
NO3(-)ChEBI
NO3ChEBI
NITRic acid ionGenerator
Nitric acid(1-)Generator
Nitric acidGenerator
Econazole nitrateHMDB
Femstat 3HMDB
GaniteHMDB
Gynazole-1HMDB
IsordilHMDB
Isosorbide dinitrateHMDB
SorbitrateHMDB
TrioxidonitrateHMDB
TrioxonitrateHMDB
NitratesMeSH, HMDB
Molecular FormulaNO3
Average Mass62.0049
Monoisotopic Mass61.987817871
IUPAC Namenitrate
Traditional Namenitrate
CAS Registry Number14797-55-8
SMILES
[O-]N(=O)=O
InChI Identifier
InChI=1S/NO3/c2-1(3)4/q-1
InChI KeyNHNBFGGVMKEFGY-UHFFFAOYSA-N