Hmdb loader

Showing metabocard for 5-Phenyl-1,3-pentadiyne (HMDB0032948)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:52:51 UTC
Update Date2022-03-07 02:53:31 UTC
HMDB IDHMDB0032948
Secondary Accession Numbers
  • HMDB32948
Metabolite Identification
Common Name5-Phenyl-1,3-pentadiyne
Description5-Phenyl-1,3-pentadiyne belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene. 5-Phenyl-1,3-pentadiyne has been detected, but not quantified in, herbs and spices. This could make 5-phenyl-1,3-pentadiyne a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 5-Phenyl-1,3-pentadiyne.
Structure
Data?1563862330
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032948 (5-Phenyl-1,3-pentadiyne)


  Mrv0541 05061306492D          

 11 11  0  0  0  0            999 V2000
   -2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
  3  2  1  0  0  0  0
  5  3  3  0  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  2  0  0  0  0
 11  8  1  0  0  0  0
 11  9  2  0  0  0  0
 11 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0032948 (5-Phenyl-1,3-pentadiyne)

HMDB0032948
     RDKit          3D
5-Phenyl-1,3-pentadiyne
 19 19  0  0  0  0  0  0  0  0999 V2000
   -5.0991   -1.1105    0.4711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0385   -0.6941    0.0523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8028   -0.1982   -0.4448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7587    0.2410   -0.8578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4972    0.7981   -1.3551 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6517    0.4240   -0.4928 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0375    1.2094    0.5736 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1024    0.8803    1.3880 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8304   -0.2712    1.1547 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4569   -1.0681    0.0913 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3853   -0.7294   -0.7218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0299   -1.4661    0.8383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5370    1.9016   -1.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3580    0.3970   -2.3753 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4677    2.1161    0.7608 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3816    1.5158    2.2169 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6741   -0.5645    1.7721 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0284   -1.9777   -0.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1053   -1.3667   -1.5530 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  3  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11  6  1  0
  1 12  1  0
  5 13  1  0
  5 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
 10 18  1  0
 11 19  1  0
M  END
Download

3D SDF for HMDB0032948 (5-Phenyl-1,3-pentadiyne)


  Mrv0541 05061306492D          

 11 11  0  0  0  0            999 V2000
   -2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
  3  2  1  0  0  0  0
  5  3  3  0  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  2  0  0  0  0
 11  8  1  0  0  0  0
 11  9  2  0  0  0  0
 11 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032948

> <DATABASE_NAME>
hmdb

> <SMILES>
C#CC#CCC1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C11H8/c1-2-3-5-8-11-9-6-4-7-10-11/h1,4,6-7,9-10H,8H2

> <INCHI_KEY>
ZZGANZXITREHOP-UHFFFAOYSA-N

> <FORMULA>
C11H8

> <MOLECULAR_WEIGHT>
140.1812

> <EXACT_MASS>
140.062600256

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
16.25374864486097

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
penta-2,4-diyn-1-ylbenzene

> <ALOGPS_LOGP>
3.47

> <JCHEM_LOGP>
3.042493766333333

> <ALOGPS_LOGS>
-4.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
47.32620000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.31e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
penta-2,4-diyn-1-ylbenzene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0032948 (5-Phenyl-1,3-pentadiyne)

HMDB0032948
     RDKit          3D
5-Phenyl-1,3-pentadiyne
 19 19  0  0  0  0  0  0  0  0999 V2000
   -5.0991   -1.1105    0.4711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0385   -0.6941    0.0523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8028   -0.1982   -0.4448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7587    0.2410   -0.8578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4972    0.7981   -1.3551 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6517    0.4240   -0.4928 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0375    1.2094    0.5736 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1024    0.8803    1.3880 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8304   -0.2712    1.1547 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4569   -1.0681    0.0913 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3853   -0.7294   -0.7218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0299   -1.4661    0.8383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5370    1.9016   -1.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3580    0.3970   -2.3753 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4677    2.1161    0.7608 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3816    1.5158    2.2169 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6741   -0.5645    1.7721 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0284   -1.9777   -0.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1053   -1.3667   -1.5530 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  3  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11  6  1  0
  1 12  1  0
  5 13  1  0
  5 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
 10 18  1  0
 11 19  1  0
M  END
Download

PDB for HMDB0032948 (5-Phenyl-1,3-pentadiyne)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    5                                                       
CONECT    4    6    7                                                       
CONECT    5    3    8                                                       
CONECT    6    4    9                                                       
CONECT    7    4   10                                                       
CONECT    8    5   11                                                       
CONECT    9    6   11                                                       
CONECT   10    7   11                                                       
CONECT   11    8    9   10                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
Download

3D PDB for HMDB0032948 (5-Phenyl-1,3-pentadiyne)

COMPND    HMDB0032948
HETATM    1  C1  UNL     1      -5.099  -1.111   0.471  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.039  -0.694   0.052  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.803  -0.198  -0.445  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.759   0.241  -0.858  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.497   0.798  -1.355  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.652   0.424  -0.493  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.037   1.209   0.574  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.102   0.880   1.388  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.830  -0.271   1.155  1.00  0.00           C  
HETATM   10  C10 UNL     1       2.457  -1.068   0.091  1.00  0.00           C  
HETATM   11  C11 UNL     1       1.385  -0.729  -0.722  1.00  0.00           C  
HETATM   12  H1  UNL     1      -6.030  -1.466   0.838  1.00  0.00           H  
HETATM   13  H2  UNL     1      -0.537   1.902  -1.422  1.00  0.00           H  
HETATM   14  H3  UNL     1      -0.358   0.397  -2.375  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.468   2.116   0.761  1.00  0.00           H  
HETATM   16  H5  UNL     1       2.382   1.516   2.217  1.00  0.00           H  
HETATM   17  H6  UNL     1       3.674  -0.565   1.772  1.00  0.00           H  
HETATM   18  H7  UNL     1       3.028  -1.978  -0.097  1.00  0.00           H  
HETATM   19  H8  UNL     1       1.105  -1.367  -1.553  1.00  0.00           H  
CONECT    1    2    2    2   12
CONECT    2    3
CONECT    3    4    4    4
CONECT    4    5
CONECT    5    6   13   14
CONECT    6    7    7   11
CONECT    7    8   15
CONECT    8    9    9   16
CONECT    9   10   17
CONECT   10   11   11   18
CONECT   11   19
END
Download

SMILES for HMDB0032948 (5-Phenyl-1,3-pentadiyne)

C#CC#CCC1=CC=CC=C1
Download

INCHI for HMDB0032948 (5-Phenyl-1,3-pentadiyne)

InChI=1S/C11H8/c1-2-3-5-8-11-9-6-4-7-10-11/h1,4,6-7,9-10H,8H2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
2,4-Pentadiynylbenzene, 9ciHMDB
BenzyldiacetyleneHMDB
Chemical FormulaC11H8
Average Molecular Weight140.1812
Monoisotopic Molecular Weight140.062600256
IUPAC Namepenta-2,4-diyn-1-ylbenzene
Traditional Namepenta-2,4-diyn-1-ylbenzene
CAS Registry Number41268-41-1
SMILES
C#CC#CCC1=CC=CC=C1
InChI Identifier
InChI=1S/C11H8/c1-2-3-5-8-11-9-6-4-7-10-11/h1,4,6-7,9-10H,8H2
InChI KeyZZGANZXITREHOP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassNot Available
Direct ParentBenzene and substituted derivatives
Alternative Parents
Substituents
  • Monocyclic benzene moiety
  • Aromatic hydrocarbon
  • Acetylide
  • Unsaturated hydrocarbon
  • Acetylene
  • Hydrocarbon
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility77.57 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.013 g/LALOGPS
logP3.47ALOGPS
logP3.04ChemAxon
logS-4ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity47.33 m³·mol⁻¹ChemAxon
Polarizability16.25 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+133.42631661259
DarkChem[M-H]-131.25731661259
DeepCCS[M+H]+124.99330932474
DeepCCS[M-H]-121.87630932474
DeepCCS[M-2H]-158.71330932474
DeepCCS[M+Na]+133.99830932474
AllCCS[M+H]+125.132859911
AllCCS[M+H-H2O]+120.432859911
AllCCS[M+NH4]+129.632859911
AllCCS[M+Na]+130.932859911
AllCCS[M-H]-123.532859911
AllCCS[M+Na-2H]-124.532859911
AllCCS[M+HCOO]-125.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. 7.39 minutes32390414
Predicted by Siyang on May 30, 202217.498 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.33 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2159.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid702.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid272.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid471.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid356.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid839.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid879.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)333.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1488.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid535.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1493.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid506.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid309.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate656.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA469.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water90.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Phenyl-1,3-pentadiyneC#CC#CCC1=CC=CC=C12138.6Standard polar33892256
5-Phenyl-1,3-pentadiyneC#CC#CCC1=CC=CC=C11311.4Standard non polar33892256
5-Phenyl-1,3-pentadiyneC#CC#CCC1=CC=CC=C11264.7Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB010933
KNApSAcK IDC00054204
Chemspider ID510444
KEGG Compound IDC17717
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound587245
PDB IDNot Available
ChEBI ID81290
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1832601
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .