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Showing metabocard for Pediocin 5 (HMDB0303658)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 03:37:43 UTC
Update Date2021-09-24 03:37:43 UTC
HMDB IDHMDB0303658
Secondary Accession NumbersNone
Metabolite Identification
Common NamePediocin 5
DescriptionNeopentane, also known as (CH3)4C, belongs to the class of organic compounds known as branched alkanes. These are acyclic branched hydrocarbons having the general formula CnH2n+2. Based on a literature review a significant number of articles have been published on Neopentane.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303658 (Pediocin 5)


  Mrv0541 02241205122D          

  5  4  0  0  0  0            999 V2000
    0.8250   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
M  END
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3D MOL for HMDB0303658 (Pediocin 5)

HMDB0303658
     RDKit          3D
Pediocin 5
 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.1774    0.9209   -0.3639 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0506    0.0030   -0.0308 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2578    0.7593    0.0504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3151   -0.6201    1.3229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1332   -1.1160   -1.0161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7060    0.6732   -1.2948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7826    1.9699   -0.4361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9343    0.9635    0.4657 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1031    1.7989   -0.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411    0.3192   -0.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6681    0.7760    1.0723 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4923   -1.3805    1.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1699    0.1579    2.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3265   -1.0811    1.3741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7857   -1.4898   -1.4623 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8273   -0.7414   -1.8116 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7253   -1.9127   -0.4782 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  1  6  1  0
  1  7  1  0
  1  8  1  0
  3  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  5 17  1  0
M  END
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3D SDF for HMDB0303658 (Pediocin 5)


  Mrv0541 02241205122D          

  5  4  0  0  0  0            999 V2000
    0.8250   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0303658

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C5H12/c1-5(2,3)4/h1-4H3

> <INCHI_KEY>
CRSOQBOWXPBRES-UHFFFAOYSA-N

> <FORMULA>
C5H12

> <MOLECULAR_WEIGHT>
72.1488

> <EXACT_MASS>
72.093900384

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
9.981098252467408

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,2-dimethylpropane

> <ALOGPS_LOGP>
2.95

> <JCHEM_LOGP>
2.3844981140000003

> <ALOGPS_LOGS>
-2.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
24.6289

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.53e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
neopentane

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0303658 (Pediocin 5)

HMDB0303658
     RDKit          3D
Pediocin 5
 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.1774    0.9209   -0.3639 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0506    0.0030   -0.0308 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2578    0.7593    0.0504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3151   -0.6201    1.3229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1332   -1.1160   -1.0161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7060    0.6732   -1.2948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7826    1.9699   -0.4361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9343    0.9635    0.4657 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1031    1.7989   -0.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411    0.3192   -0.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6681    0.7760    1.0723 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4923   -1.3805    1.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1699    0.1579    2.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3265   -1.0811    1.3741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7857   -1.4898   -1.4623 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8273   -0.7414   -1.8116 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7253   -1.9127   -0.4782 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  1  6  1  0
  1  7  1  0
  1  8  1  0
  3  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  5 17  1  0
M  END
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PDB for HMDB0303658 (Pediocin 5)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.540  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.080   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0303658 (Pediocin 5)

COMPND    HMDB0303658
HETATM    1  C1  UNL     1      -1.177   0.921  -0.364  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.051   0.003  -0.031  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.258   0.759   0.050  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.315  -0.620   1.323  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.133  -1.116  -1.016  1.00  0.00           C  
HETATM    6  H1  UNL     1      -1.706   0.673  -1.295  1.00  0.00           H  
HETATM    7  H2  UNL     1      -0.783   1.970  -0.436  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.934   0.963   0.466  1.00  0.00           H  
HETATM    9  H4  UNL     1       1.103   1.799  -0.340  1.00  0.00           H  
HETATM   10  H5  UNL     1       2.041   0.319  -0.615  1.00  0.00           H  
HETATM   11  H6  UNL     1       1.668   0.776   1.072  1.00  0.00           H  
HETATM   12  H7  UNL     1       0.492  -1.381   1.475  1.00  0.00           H  
HETATM   13  H8  UNL     1      -0.170   0.158   2.088  1.00  0.00           H  
HETATM   14  H9  UNL     1      -1.327  -1.081   1.374  1.00  0.00           H  
HETATM   15  H10 UNL     1      -0.786  -1.490  -1.462  1.00  0.00           H  
HETATM   16  H11 UNL     1       0.827  -0.741  -1.812  1.00  0.00           H  
HETATM   17  H12 UNL     1       0.725  -1.913  -0.478  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    4    5
CONECT    3    9   10   11
CONECT    4   12   13   14
CONECT    5   15   16   17
END
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SMILES for HMDB0303658 (Pediocin 5)

CC(C)(C)C
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INCHI for HMDB0303658 (Pediocin 5)

InChI=1S/C5H12/c1-5(2,3)4/h1-4H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(CH3)4CChEBI
Chemical FormulaC5H12
Average Molecular Weight72.1488
Monoisotopic Molecular Weight72.093900384
IUPAC Name2,2-dimethylpropane
Traditional Nameneopentane
CAS Registry NumberNot Available
SMILES
CC(C)(C)C
InChI Identifier
InChI=1S/C5H12/c1-5(2,3)4/h1-4H3
InChI KeyCRSOQBOWXPBRES-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as branched alkanes. These are acyclic branched hydrocarbons having the general formula CnH2n+2.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassSaturated hydrocarbons
Sub ClassAlkanes
Direct ParentBranched alkanes
Alternative ParentsNot Available
Substituents
  • Branched alkane
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP2.95ALOGPS
logP2.38ChemAxon
logS-2.3ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24.63 m³·mol⁻¹ChemAxon
Polarizability9.98 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+116.44432859911
AllCCS[M+H-H2O]+112.11432859911
AllCCS[M+Na]+121.65532859911
AllCCS[M+NH4]+120.48832859911
AllCCS[M-H]-127.39432859911
AllCCS[M+Na-2H]-133.11632859911
AllCCS[M+HCOO]-139.39932859911
DeepCCS[M+H]+126.30130932474
DeepCCS[M-H]-123.78830932474
DeepCCS[M-2H]-159.98930932474
DeepCCS[M+Na]+134.77930932474

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
MSMass Spectrum (Electron Ionization)splash10-0a6r-9000000000-0e59d94dbc9a59710b3a2014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 10V, Positive-QTOFsplash10-00di-9000000000-cae6782a13dc826484962016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 20V, Positive-QTOFsplash10-00di-9000000000-9ff95a012a0cf9d59acc2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 40V, Positive-QTOFsplash10-00di-9000000000-f9d0c03766c5996af08f2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 10V, Negative-QTOFsplash10-00di-9000000000-ad55f8a26d586dfe5dd32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 20V, Negative-QTOFsplash10-00di-9000000000-ad55f8a26d586dfe5dd32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 40V, Negative-QTOFsplash10-00di-9000000000-c172f76625b1193e785a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 10V, Positive-QTOFsplash10-00di-9000000000-7d3784284a32d01a81d02021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 20V, Positive-QTOFsplash10-05fr-9000000000-2a4f6688a11db7267de42021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 40V, Positive-QTOFsplash10-052f-9000000000-8626096591b8f582f3852021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 10V, Negative-QTOFsplash10-00di-9000000000-6e73363b636fec5933cb2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 20V, Negative-QTOFsplash10-00di-9000000000-6e73363b636fec5933cb2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pediocin 5 40V, Negative-QTOFsplash10-00di-9000000000-6e73363b636fec5933cb2021-10-21Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Biological Properties
Cellular LocationsNot Available
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 IDFDB017589
KNApSAcK IDNot Available
Chemspider ID9646
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID30358
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available