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Showing NP-Card for Imidazole (NP0000920)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:40:16 UTC
NP-MRD IDNP0000920
Secondary Accession NumbersNone
Natural Product Identification
Common NameImidazole
DescriptionImidazole is an organic compound with the formula C3N2H4. It is a white or colourless solid that is soluble in water, producing a mildly alkaline solution. In chemistry, it is an aromatic heterocycle, classified as a diazole, and has non-adjacent nitrogen atoms. Imidazole is a heterocyclic aromatic organic compound. It is classified as an alkaloid. The ring system of the molecule is present in important biological building blocks such as histidine and histamine. Imidazole can act as a base and as a weak acid. Imidazole exists in two tautomeric forms with the hydrogen atom moving between the two nitrogens. Many drugs contain an imidazole ring, such as antifungal drugs and nitroimidazole. Imidazole is a 5 membered planar ring which is soluble in water and polar solvents. Imidazole is a base and an excellent nucleophile. It reacts at the NH nitrogen, attacking alkylating and acylating compounds. It is not particularly susceptible to electrophilic attacks at the carbon atoms, and most of these reactions are substitutions that keep the aromaticity intact. One can see from the resonance structure that the carbon-2 is the carbon most likely to have a nucleophile attack it, but in general nucleophilic substitutions are difficult with imidazole. Imidazole is incorporated into many important biological molecules. The most obvious is the amino acid histidine, which has an imidazole side chain. Histidine is present in many proteins and enzymes and plays a vital part in the structure and binding functions of hemoglobin.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000920 (Imidazole)


  Mrv1652305271900162D          

  5  5  0  0  0  0            999 V2000
   13.0661  -12.4506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0661  -13.2756    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.8507  -13.5305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3357  -12.8631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8507  -12.1957    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  1  1  0  0  0  0
M  END
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3D MOL for NP0000920 (Imidazole)

HMDB0001525
     RDKit          3D
Imidazole
  9  9  0  0  0  0  0  0  0  0999 V2000
    1.1113   -0.5950   -0.0207 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6600    0.7059    0.0233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6991    0.6701    0.0230 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0764   -0.6188   -0.0201 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0202   -1.3984   -0.0470 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1366   -0.9583   -0.0336 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2859    1.5855    0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3138    1.4930    0.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1245   -0.8840   -0.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  1  1  0
  1  6  1  0
  2  7  1  0
  3  8  1  0
  4  9  1  0
M  END
Download

3D SDF for NP0000920 (Imidazole)


  Mrv1652305271900162D          

  5  5  0  0  0  0            999 V2000
   13.0661  -12.4506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0661  -13.2756    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.8507  -13.5305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3357  -12.8631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8507  -12.1957    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  1  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000920

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N1C=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)

> <INCHI_KEY>
RAXXELZNTBOGNW-UHFFFAOYSA-N

> <FORMULA>
C3H4N2

> <MOLECULAR_WEIGHT>
68.0773

> <EXACT_MASS>
68.037448138

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
6.556334183945702

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-imidazole

> <ALOGPS_LOGP>
-0.21

> <JCHEM_LOGP>
-0.145224207

> <ALOGPS_LOGS>
0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.396939092733913

> <JCHEM_PKA_STRONGEST_BASIC>
6.967149345274132

> <JCHEM_POLAR_SURFACE_AREA>
28.68

> <JCHEM_REFRACTIVITY>
19.0128

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.38e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
imidazole

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0000920 (Imidazole)

HMDB0001525
     RDKit          3D
Imidazole
  9  9  0  0  0  0  0  0  0  0999 V2000
    1.1113   -0.5950   -0.0207 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6600    0.7059    0.0233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6991    0.6701    0.0230 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0764   -0.6188   -0.0201 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0202   -1.3984   -0.0470 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1366   -0.9583   -0.0336 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2859    1.5855    0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3138    1.4930    0.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1245   -0.8840   -0.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  1  1  0
  1  6  1  0
  2  7  1  0
  3  8  1  0
  4  9  1  0
M  END
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PDB for NP0000920 (Imidazole)

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      24.390 -23.241   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      24.390 -24.781   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      25.855 -25.257   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      26.760 -24.011   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      25.855 -22.765   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for NP0000920 (Imidazole)

COMPND    HMDB0001525
HETATM    1  C1  UNL     1       1.111  -0.595  -0.021  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.660   0.706   0.023  1.00  0.00           C  
HETATM    3  N1  UNL     1      -0.699   0.670   0.023  1.00  0.00           N  
HETATM    4  C3  UNL     1      -1.076  -0.619  -0.020  1.00  0.00           C  
HETATM    5  N2  UNL     1       0.020  -1.398  -0.047  1.00  0.00           N  
HETATM    6  H1  UNL     1       2.137  -0.958  -0.034  1.00  0.00           H  
HETATM    7  H2  UNL     1       1.286   1.585   0.052  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.314   1.493   0.051  1.00  0.00           H  
HETATM    9  H4  UNL     1      -2.125  -0.884  -0.028  1.00  0.00           H  
CONECT    1    2    2    5    6
CONECT    2    3    7
CONECT    3    4    8
CONECT    4    5    5    9
END
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SMILES for NP0000920 (Imidazole)

N1C=CN=C1
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INCHI for NP0000920 (Imidazole)

InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)
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View in JSmol
Synonyms
ValueSource
1,3-Diaza-2,4-cyclopentadieneChEBI
1,3-DiazoleChEBI
GlyoxalineChEBI
HimChEBI
IMDChEBI
ImidazolChEBI
IminazoleChEBI
MiazoleChEBI
N,N'-1,2-ethenediylmethanimidamideChEBI
N,N'-vinyleneformamidineChEBI
Pyrro[b]monazoleChEBI
1H-ImidazoleHMDB
GlyoxalinHMDB
ImutexHMDB
Pyrro(b)monazoleHMDB
{Pyrro[b]monazole}HMDB
Imidazole acetateHMDB
Imidazole monophosphonateHMDB
Imidazole sodiumHMDB
Imidazolium chlorideHMDB
Al-imidazoleHMDB
Imidazole citrateHMDB
Cu-imidazoleHMDB
Imidazole conjugate monoacidHMDB
Imidazole monohydrochlorideHMDB
ImidazoleChEBI
Chemical FormulaC3H4N2
Average Mass68.0773 Da
Monoisotopic Mass68.03745 Da
IUPAC Name1H-imidazole
Traditional Nameimidazole
CAS Registry Number288-32-4
SMILES
N1C=CN=C1
InChI Identifier
InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)
InChI KeyRAXXELZNTBOGNW-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, 400 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, 500 MHz, DMSO, simulated)Anonymous2021-08-05View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, Methanol, simulated)Varshavi.d262021-07-14View Spectrum
Species
Species of Origin
Species NameSourceReference
Lens culinarisKNApSAcK Database
Lens culinaris Medik.NULL
    • Imidazole, a new natural product from the leguminosae. Phytochemistry, Volume 26, Issue 12, 1987,...
Macrotyloma uniflorumKNApSAcK Database
Psophocarpus tetragonolobusKNApSAcK Database
Vigna radiataKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as imidazoles. Imidazoles are compounds containing an imidazole ring, which is an aromatic five-member ring with two nitrogen atoms at positions 1 and 3, and three carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzoles
Sub ClassImidazoles
Direct ParentImidazoles
Alternative Parents
Substituents
  • Heteroaromatic compound
  • Imidazole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point90.5 °CNot Available
Boiling Point257.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility159100 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.08Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility538 g/LALOGPS
logP-0.21ALOGPS
logP-0.15ChemAxon
logS0.9ALOGPS
pKa (Strongest Acidic)13.4ChemAxon
pKa (Strongest Basic)6.97ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area28.68 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity19.01 m³·mol⁻¹ChemAxon
Polarizability6.56 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001525
DrugBank IDDB03366
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012307
KNApSAcK IDC00054098
Chemspider ID773
KEGG Compound IDC01589
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkImidazole
METLIN ID4190
PubChem Compound795
PDB IDNot Available
ChEBI ID16069
Good Scents IDrw1251201
References
General References
  1. Bruynseels J, De Coster R, Van Rooy P, Wouters W, Coene MC, Snoeck E, Raeymaekers A, Freyne E, Sanz G, Vanden Bussche G, et al.: R 75251, a new inhibitor of steroid biosynthesis. Prostate. 1990;16(4):345-57. [PubMed:2164659 ]
  2. Sheu JR, Hsiao G, Shen MY, Lin WY, Tzeng CR: The hyperaggregability of platelets from normal pregnancy is mediated through thromboxane A2 and cyclic AMP pathways. Clin Lab Haematol. 2002 Apr;24(2):121-9. [PubMed:11985559 ]
  3. Lamberts SW, Bruining HA, Marzouk H, Zuiderwijk J, Uitterlinden P, Blijd JJ, Hackeng WH, De Jong FH: The new aromatase inhibitor CGS-16949A suppresses aldosterone and cortisol production by human adrenal cells in vitro. J Clin Endocrinol Metab. 1989 Oct;69(4):896-901. [PubMed:2550511 ]
  4. Luft FC, Mann JF: New classes of antihypertensive drugs and new findings with established agents. Curr Opin Nephrol Hypertens. 1992 Oct;1(1):91-9. [PubMed:1365836 ]
  5. Allolio B, Stuttmann R, Winkelmann W: Missing effect of etomidate on testosterone secretion in man. Klin Wochenschr. 1986 Jan 15;64(2):86-8. [PubMed:3005757 ]
  6. Schraag S, Pawlik M, Mohl U, Bohm BO, Georgieff M: The role of ascorbic acid and xylitol in etomidate-induced adrenocortical suppression in humans. Eur J Anaesthesiol. 1996 Jul;13(4):346-51. [PubMed:8842654 ]
  7. Cotovio J, Roguet R, Pion FX, Rougier A, Leclaire J: Effect of imidazole derivatives on cytochrome P-450 enzyme activities in a reconstructed human epidermis. Skin Pharmacol. 1996;9(4):242-9. [PubMed:8896115 ]
  8. Kuhlkamp V, Schmid F, Ress KM, Kramer BK, Mayer F, Liebich HM, Risler T, Seipel L: Quantification of cibenzoline and its imidazole metabolite by high-performance liquid chromatography in human serum. J Chromatogr. 1990 Jun 8;528(1):267-73. [PubMed:2384563 ]
  9. Santella RM, Yang XY, Hsieh LL, Young TL: Immunologic methods for the detection of carcinogen adducts in humans. Prog Clin Biol Res. 1990;340C:247-57. [PubMed:2199982 ]
  10. Howden CW, Kenyon CJ, Beastall GH, Reid JL: Inhibition by omeprazole of adrenocortical response to ACTH: clinical studies and experiments on bovine adrenal cortex in vitro. Clin Sci (Lond). 1986 Jan;70(1):99-102. [PubMed:3002707 ]
  11. Baynes J, Levine M: Urea-extractable protein from human epidermis. Biochim Biophys Acta. 1976 Jul 19;439(1):107-15. [PubMed:952948 ]
  12. Shishu, Singla AK, Kaur IP: Inhibitory effect of dibenzoylmethane on mutagenicity of food-derived heterocyclic amine mutagens. Phytomedicine. 2003;10(6-7):575-82. [PubMed:13678246 ]
  13. Caccuri AM, Ascenzi P, Lo Bello M, Federici G, Battistoni A, Mazzetti P, Ricci G: Are the steady state kinetics of glutathione transferase always dependent on the deprotonation of the bound glutathione? New insights in the kinetic mechanism of GST P 1-1. Biochem Biophys Res Commun. 1994 May 16;200(3):1428-34. [PubMed:8185596 ]
  14. Vanden Bossche H, Marichal P, Gorrens J, Coene MC, Willemsens G, Bellens D, Roels I, Moereels H, Janssen PA: Biochemical approaches to selective antifungal activity. Focus on azole antifungals. Mycoses. 1989;32 Suppl 1:35-52. [PubMed:2561184 ]
  15. Smith DP, Smith DG, Curtain CC, Boas JF, Pilbrow JR, Ciccotosto GD, Lau TL, Tew DJ, Perez K, Wade JD, Bush AI, Drew SC, Separovic F, Masters CL, Cappai R, Barnham KJ: Copper-mediated amyloid-beta toxicity is associated with an intermolecular histidine bridge. J Biol Chem. 2006 Jun 2;281(22):15145-54. Epub 2006 Apr 4. [PubMed:16595673 ]