Showing NP-Card for Histamine (NP0001365)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2025-02-11 15:41:15 UTC
NP-MRD IDNP0001365
Secondary Accession NumbersNone
Natural Product Identification
Common NameHistamine
DescriptionHistamine is an amine derived by enzymatic decarboxylation of histidine. It is a powerful stimulant of gastric secretion, a constrictor of bronchial smooth muscle, a vasodilator, and also a centrally acting neurotransmitter. Histamine can be found in Photobacterium phosphoreum and Lactobacillus (PMID: 17066936 ). Histamine belongs to the class of organic compounds known as 2-arylethylamines. These are primary amines that have the general formula RCCNH2, where R is an organic group. High amounts of histamine have been found in spinach, oats and ryes. Another foods such as green beans, broccoli, and beetroots also contain histamine but in lower concentrations. Histamine has also been detected but not quantified in several different foods, such as groundcherries, carobs, bok choy, biscuits, and longans.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001365 (Histamine)

  Mrv1652309042000132D          

  8  8  0  0  0  0            999 V2000
10000.301210000.5262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.016010000.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.728710000.5262    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.915610000.6081    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.248210000.1231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5031 9999.3385    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3281 9999.3385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.583010000.1231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  7  8  2  0  0  0  0
  4  5  2  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
Download

3D MOL for NP0001365 (Histamine)

HMDB0000870
     RDKit          3D
Histamine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.9568   -0.4732   -0.3723 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5252   -0.6604   -0.3978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8874    0.6814   -0.1322 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6031    0.5068   -0.1549 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3117   -0.6449   -0.3735 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6061   -0.3157   -0.2997 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7572    0.9939   -0.0439 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5137    1.4928    0.0437 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4195   -1.0322    0.3628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2418    0.5204   -0.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1874   -1.4115    0.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1587   -1.0044   -1.3875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1475    1.3595   -0.9559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2225    1.1453    0.8016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8595   -1.6177   -0.5660 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3764   -1.0199   -0.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7190    1.4799    0.0578 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  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  4  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
M  END
Download

3D SDF for NP0001365 (Histamine)

  Mrv1652309042000132D          

  8  8  0  0  0  0            999 V2000
10000.301210000.5262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.016010000.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.728710000.5262    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.915610000.6081    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.248210000.1231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5031 9999.3385    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3281 9999.3385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.583010000.1231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  7  8  2  0  0  0  0
  4  5  2  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001365

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCC1=CNC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H9N3/c6-2-1-5-3-7-4-8-5/h3-4H,1-2,6H2,(H,7,8)

> <INCHI_KEY>
NTYJJOPFIAHURM-UHFFFAOYSA-N

> <FORMULA>
C5H9N3

> <MOLECULAR_WEIGHT>
111.1451

> <EXACT_MASS>
111.079647303

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.083995477047418

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(1H-imidazol-4-yl)ethan-1-amine

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
-0.7009711443333334

> <ALOGPS_LOGS>
0.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.456615295256658

> <JCHEM_PKA_STRONGEST_BASIC>
9.576453109401491

> <JCHEM_POLAR_SURFACE_AREA>
54.7

> <JCHEM_REFRACTIVITY>
31.663399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.69e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
histamine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001365 (Histamine)

HMDB0000870
     RDKit          3D
Histamine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.9568   -0.4732   -0.3723 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5252   -0.6604   -0.3978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8874    0.6814   -0.1322 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6031    0.5068   -0.1549 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3117   -0.6449   -0.3735 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6061   -0.3157   -0.2997 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7572    0.9939   -0.0439 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5137    1.4928    0.0437 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4195   -1.0322    0.3628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2418    0.5204   -0.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1874   -1.4115    0.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1587   -1.0044   -1.3875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1475    1.3595   -0.9559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2225    1.1453    0.8016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8595   -1.6177   -0.5660 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3764   -1.0199   -0.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7190    1.4799    0.0578 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  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  4  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
M  END
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PDB for NP0001365 (Histamine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8667.2298667.649   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8668.5638666.880   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0    8669.8948667.649   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0    8664.6428667.802   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0    8663.3978666.896   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8663.8728665.432   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8665.4128665.432   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8665.8888666.896   0.000  0.00  0.00           C+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2                                                            
CONECT    4    5    8                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    8    6                                                       
CONECT    8    7    4    1                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for NP0001365 (Histamine)

COMPND    HMDB0000870
HETATM    1  N1  UNL     1      -2.957  -0.473  -0.372  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.525  -0.660  -0.398  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.887   0.681  -0.132  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.603   0.507  -0.155  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.312  -0.645  -0.373  1.00  0.00           C  
HETATM    6  N2  UNL     1       2.606  -0.316  -0.300  1.00  0.00           N  
HETATM    7  C5  UNL     1       2.757   0.994  -0.044  1.00  0.00           C  
HETATM    8  N3  UNL     1       1.514   1.493   0.044  1.00  0.00           N  
HETATM    9  H1  UNL     1      -3.419  -1.032   0.363  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.242   0.520  -0.241  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.187  -1.411   0.344  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.159  -1.004  -1.388  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.147   1.359  -0.956  1.00  0.00           H  
HETATM   14  H6  UNL     1      -1.222   1.145   0.802  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.860  -1.618  -0.566  1.00  0.00           H  
HETATM   16  H8  UNL     1       3.376  -1.020  -0.431  1.00  0.00           H  
HETATM   17  H9  UNL     1       3.719   1.480   0.058  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5    5    8
CONECT    5    6   15
CONECT    6    7   16
CONECT    7    8    8   17
END
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SMILES for NP0001365 (Histamine)

NCCC1=CNC=N1
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INCHI for NP0001365 (Histamine)

InChI=1S/C5H9N3/c6-2-1-5-3-7-4-8-5/h3-4H,1-2,6H2,(H,7,8)
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View in JSmol
Synonyms
Chemical FormulaC5H9N3
Average Mass111.1451 Da
Monoisotopic Mass111.07965 Da
IUPAC Name2-(1H-imidazol-4-yl)ethan-1-amine
Traditional Namehistamine
CAS Registry Number51-45-6
SMILES
NCCC1=CNC=N1
InChI Identifier
InChI=1S/C5H9N3/c6-2-1-5-3-7-4-8-5/h3-4H,1-2,6H2,(H,7,8)
InChI KeyNTYJJOPFIAHURM-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View 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 EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-03View Spectrum
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 2-arylethylamines. These are primary amines that have the general formula RCCNH2, where R is an organic group.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct Parent2-arylethylamines
Alternative Parents
Substituents
  • 2-arylethylamine
  • Aralkylamine
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Organoheterocyclic compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point86 °CNot Available
Boiling Point380.29 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.70Sangster, J. (1993). LOGKOW- a Databank of Evaluated Octanol-Water Partition Coefficients. Sangster Research Laboratories, Montreal.
Predicted Properties
PropertyValueSource
Water Solubility169 g/LALOGPS
logP-0.69ALOGPS
logP-0.7ChemAxon
logS0.18ALOGPS
pKa (Strongest Acidic)14.46ChemAxon
pKa (Strongest Basic)9.58ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area54.7 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity31.66 m³·mol⁻¹ChemAxon
Polarizability12.08 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000870
DrugBank IDDB05381
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012596
KNApSAcK IDC00001414
Chemspider ID753
KEGG Compound IDC00388
BioCyc IDHISTAMINE
BiGG ID1810403
Wikipedia LinkHistamine
METLIN ID68
PubChem Compound774
PDB IDNot Available
ChEBI ID18295
Good Scents IDrw1250321
References
General References