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Showing metabocard for Pentyl formate (HMDB0040327)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:51:36 UTC
Update Date2023-02-21 17:28:09 UTC
HMDB IDHMDB0040327
Secondary Accession Numbers
  • HMDB40327
Metabolite Identification
Common NamePentyl formate
DescriptionPentyl formate, also known as amyl methanoate or fema 2068, belongs to the class of organic compounds known as carboxylic acid esters. These are carboxylic acid derivatives in which the carbon atom from the carbonyl group is attached to an alkyl or an aryl moiety through an oxygen atom (forming an ester group). Pentyl formate is an earthy, ethereal, and fruity tasting compound. Pentyl formate is found, on average, in the highest concentration in cow milk. Pentyl formate has also been detected, but not quantified, in a few different foods, such as alcoholic beverages, strawberries, garden tomatoes, fried cured pork, cognac and honey.
Structure
Data?1677000489
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040327 (Pentyl formate)


  Mrv1652305271900252D          

  8  7  0  0  0  0            999 V2000
   -3.0789   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2211   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4934   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  7  6  2  0  0  0  0
  8  5  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
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3D MOL for HMDB0040327 (Pentyl formate)

HMDB0040327
     RDKit          3D
Pentyl formate
 20 19  0  0  0  0  0  0  0  0999 V2000
    2.3996    0.8870    0.2845 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9460    0.2551   -1.0284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4437    0.0805   -0.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0676   -0.8110    0.2271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4330   -0.9889    0.3279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9921    0.2969    0.5153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3682    0.4815    0.6462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0723   -0.5645    0.5867 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4948    0.0987    1.0526 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3429    1.4392    0.1185 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6323    1.6299    0.5781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2102    0.9865   -1.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4648   -0.6785   -1.2549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0711    1.0430   -0.8275 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1068   -0.3761   -1.8863 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4414   -0.3110    1.1574 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5935   -1.7873    0.1809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6638   -1.6854    1.1595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7925   -1.4627   -0.6153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7506    1.4671    0.7861 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  7 20  1  0
M  END
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3D SDF for HMDB0040327 (Pentyl formate)


  Mrv1652305271900252D          

  8  7  0  0  0  0            999 V2000
   -3.0789   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2211   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4934   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  7  6  2  0  0  0  0
  8  5  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040327

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCOC=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O2/c1-2-3-4-5-8-6-7/h6H,2-5H2,1H3

> <INCHI_KEY>
DIQMPQMYFZXDAX-UHFFFAOYSA-N

> <FORMULA>
C6H12O2

> <MOLECULAR_WEIGHT>
116.1583

> <EXACT_MASS>
116.083729628

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.359891710086064

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentyl formate

> <ALOGPS_LOGP>
2.10

> <JCHEM_LOGP>
1.6423173133333335

> <ALOGPS_LOGS>
-1.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.816465891809667

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
31.396900000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.09e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
formic acid, pentyl ester

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0040327 (Pentyl formate)

HMDB0040327
     RDKit          3D
Pentyl formate
 20 19  0  0  0  0  0  0  0  0999 V2000
    2.3996    0.8870    0.2845 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9460    0.2551   -1.0284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4437    0.0805   -0.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0676   -0.8110    0.2271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4330   -0.9889    0.3279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9921    0.2969    0.5153 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3682    0.4815    0.6462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0723   -0.5645    0.5867 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4948    0.0987    1.0526 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3429    1.4392    0.1185 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6323    1.6299    0.5781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2102    0.9865   -1.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4648   -0.6785   -1.2549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0711    1.0430   -0.8275 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1068   -0.3761   -1.8863 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4414   -0.3110    1.1574 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5935   -1.7873    0.1809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6638   -1.6854    1.1595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7925   -1.4627   -0.6153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7506    1.4671    0.7861 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  7 20  1  0
M  END
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PDB for HMDB0040327 (Pentyl formate)

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      -5.747  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.414  -1.897   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.746  -1.897   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.413  -2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.255  -2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.588  -1.897   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.921  -1.897   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    8                                                       
CONECT    6    7    8                                                       
CONECT    7    6                                                            
CONECT    8    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0040327 (Pentyl formate)

COMPND    HMDB0040327
HETATM    1  C1  UNL     1       2.400   0.887   0.284  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.946   0.255  -1.028  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.444   0.080  -0.932  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.068  -0.811   0.227  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.433  -0.989   0.328  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.992   0.297   0.515  1.00  0.00           O  
HETATM    7  C6  UNL     1      -3.368   0.481   0.646  1.00  0.00           C  
HETATM    8  O2  UNL     1      -4.072  -0.564   0.587  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.495   0.099   1.053  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.343   1.439   0.119  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.632   1.630   0.578  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.210   0.986  -1.818  1.00  0.00           H  
HETATM   13  H5  UNL     1       2.465  -0.678  -1.255  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.071   1.043  -0.828  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.107  -0.376  -1.886  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.441  -0.311   1.157  1.00  0.00           H  
HETATM   17  H9  UNL     1       0.593  -1.787   0.181  1.00  0.00           H  
HETATM   18  H10 UNL     1      -1.664  -1.685   1.160  1.00  0.00           H  
HETATM   19  H11 UNL     1      -1.793  -1.463  -0.615  1.00  0.00           H  
HETATM   20  H12 UNL     1      -3.751   1.467   0.786  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3   12   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7
CONECT    7    8    8   20
END
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SMILES for HMDB0040327 (Pentyl formate)

CCCCCOC=O
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INCHI for HMDB0040327 (Pentyl formate)

InChI=1S/C6H12O2/c1-2-3-4-5-8-6-7/h6H,2-5H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Pentyl formic acidGenerator
3-Pentanol formateHMDB
Amyl formateHMDB
Amyl methanoateHMDB
FEMA 2068HMDB
Formic acid N-amyl esterHMDB
Formic acid, pentyl esterHMDB
m-Pentyl formateHMDB
Methanoic acid, pentyl esterHMDB
N-Amyl formateHMDB
N-Pentyl formateHMDB
N-Pentyl methanoateHMDB
Pentyl methanoateHMDB
Chemical FormulaC6H12O2
Average Molecular Weight116.1583
Monoisotopic Molecular Weight116.083729628
IUPAC Namepentyl formate
Traditional Nameformic acid, pentyl ester
CAS Registry Number638-49-3
SMILES
CCCCCOC=O
InChI Identifier
InChI=1S/C6H12O2/c1-2-3-4-5-8-6-7/h6H,2-5H2,1H3
InChI KeyDIQMPQMYFZXDAX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carboxylic acid esters. These are carboxylic acid derivatives in which the carbon atom from the carbonyl group is attached to an alkyl or an aryl moiety through an oxygen atom (forming an ester group).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassCarboxylic acid derivatives
Direct ParentCarboxylic acid esters
Alternative Parents
Substituents
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-73.5 °CNot Available
Boiling Point130.00 to 131.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility3066 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.905 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility4.09 g/LALOGPS
logP2.1ALOGPS
logP1.64ChemAxon
logS-1.4ALOGPS
pKa (Strongest Basic)-6.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity31.4 m³·mol⁻¹ChemAxon
Polarizability13.36 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
DarkChem[M+H]+124.02131661259
DarkChem[M-H]-120.6931661259
DeepCCS[M+H]+134.34930932474
DeepCCS[M-H]-132.31130932474
DeepCCS[M-2H]-168.20130932474
DeepCCS[M+Na]+142.72830932474
AllCCS[M+H]+128.332859911
AllCCS[M+H-H2O]+124.132859911
AllCCS[M+NH4]+132.332859911
AllCCS[M+Na]+133.432859911
AllCCS[M-H]-130.632859911
AllCCS[M+Na-2H]-133.832859911
AllCCS[M+HCOO]-137.532859911

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. Predicted by Afia on May 17, 2022.4.46 minutes32390414
Predicted by Siyang on May 30, 202212.1705 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.34 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1630.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid399.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid147.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid265.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid239.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid469.7 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 Acid530.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)116.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1011.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid348.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1147.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid336.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid342.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate448.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA344.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water61.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Pentyl formateCCCCCOC=O1101.9Standard polar33892256
Pentyl formateCCCCCOC=O802.3Standard non polar33892256
Pentyl formateCCCCCOC=O890.0Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB020050
KNApSAcK IDNot Available
Chemspider ID12012
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12529
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1015511
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.. .