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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-24 12:46:16 UTC

Update Date

2021-09-24 12:46:16 UTC

HMDB ID

HMDB0304823

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Lysozyme

Description

Preservative. Prevents late blowing in semi-hard cheeses due to Clostridium tyrobutyricum. Lysozyme is part of the innate immune system. Children fed infant formula lack lysozyme in their diet and have three times the rate of diarrheal disease.[citation needed] Since lysozyme is a natural form of protection from pathogens like Salmonella, E.coli and Pseudomonas, when it is deficient due to infant formula feeding, can lead to increased incidence of disease.; Whereas the skin is a protective barrier due to its dryness and acidity, the conjunctiva (membrane covering the eye) is instead protected by secreted enzymes, mainly lysozyme and defensin. However, when these protective barriers fail, conjunctivitis results. Lysozyme is found in garden onion, papaya, and soft-necked garlic.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0      -2.550   2.233   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.884   3.003   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.217   3.003   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.218   2.233   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.278   0.701   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.784   0.381   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.117   2.233   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.551   3.003   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -7.885   2.233   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -6.551   4.543   0.000  0.00  0.00           O+0
HETATM   11  S   UNK     0       2.554   1.715   0.000  0.00  0.00           S+0
HETATM   12  S   UNK     0       1.524   2.859   0.000  0.00  0.00           S+0
HETATM   13  H   UNK     0       0.198   3.771   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    6    7                                                       
CONECT    6    5   11                                                       
CONECT    7    3    5   12   13                                             
CONECT    8    4    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    6   12                                                       
CONECT   12    7   11                                                       
CONECT   13    7                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

COMPND    HMDB0304823
HETATM    1  N1  UNL     1       4.587   1.253   0.759  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.937   0.213   0.387  1.00  0.00           C  
HETATM    3  O1  UNL     1       4.405  -1.034   0.742  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.703   0.358  -0.413  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.571  -0.266   0.368  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.249  -0.180  -0.350  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.789  -0.834   0.532  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.173  -0.791  -0.126  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.647   0.554  -0.395  1.00  0.00           C  
HETATM   10  C8  UNL     1      -4.065   0.802  -0.322  1.00  0.00           C  
HETATM   11  S1  UNL     1      -4.932  -0.366   0.700  1.00  0.00           S  
HETATM   12  S2  UNL     1      -3.283  -1.701   0.938  1.00  0.00           S  
HETATM   13  H1  UNL     1       4.326   2.227   0.549  1.00  0.00           H  
HETATM   14  H2  UNL     1       3.859  -1.887   0.708  1.00  0.00           H  
HETATM   15  H3  UNL     1       2.870  -0.215  -1.368  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.516   1.425  -0.645  1.00  0.00           H  
HETATM   17  H5  UNL     1       1.468   0.316   1.316  1.00  0.00           H  
HETATM   18  H6  UNL     1       1.826  -1.327   0.542  1.00  0.00           H  
HETATM   19  H7  UNL     1       0.255  -0.570  -1.364  1.00  0.00           H  
HETATM   20  H8  UNL     1      -0.015   0.918  -0.381  1.00  0.00           H  
HETATM   21  H9  UNL     1      -0.831  -0.369   1.536  1.00  0.00           H  
HETATM   22  H10 UNL     1      -0.568  -1.911   0.685  1.00  0.00           H  
HETATM   23  H11 UNL     1      -2.049  -1.387  -1.071  1.00  0.00           H  
HETATM   24  H12 UNL     1      -2.261   0.881  -1.409  1.00  0.00           H  
HETATM   25  H13 UNL     1      -2.110   1.265   0.308  1.00  0.00           H  
HETATM   26  H14 UNL     1      -4.297   1.837   0.069  1.00  0.00           H  
HETATM   27  H15 UNL     1      -4.552   0.789  -1.341  1.00  0.00           H  
CONECT    1    2    2   13
CONECT    2    3    4
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9   12   23
CONECT    9   10   24   25
CONECT   10   11   26   27
CONECT   11   12
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5-(1,2-Dithiolan-3-yl)-pentanamide	MetaCyc
DL-Lipoamide	MetaCyc
6,8-Dithiooctanoic amide	MetaCyc

Chemical Formula

C₈H₁₅NOS₂

Average Molecular Weight

205.33

Monoisotopic Molecular Weight

205.059506455

IUPAC Name

5-[(3R)-1,2-dithiolan-3-yl]pentanimidic acid

Traditional Name

lipoamide

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CCCCC(O)=N)CCSS1

InChI Identifier

InChI=1S/C8H15NOS2/c9-8(10)4-2-1-3-7-5-6-11-12-7/h7H,1-6H2,(H2,9,10)/t7-/m1/s1

InChI Key

FCCDDURTIIUXBY-SSDOTTSWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lipoamides. Lipoamides are compounds containing a lipoamide moiety, which consists of a pentanamide attached to the C3 carbon atom of a 1,2-dithiolane ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dithiolanes

Sub Class

Lipoamides

Direct Parent

Lipoamides

Alternative Parents

Substituents

Lipoamide
Fatty amide
Fatty acyl
1,2-dithiolane
Carboxamide group
Organic disulfide
Primary carboxylic acid amide
Carboxylic acid derivative
Carbonyl group
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

lipoamide (CHEBI:83094 )

Ontology

Not Available

Exogenous (HMDB: HMDB0304823)

Food

Fruit

Tropical fruit

Papaya (FooDB: FOOD00041)

Vegetable

Onion-family vegetable

Garden onion (FooDB: FOOD00006)

Herb and spice

Herb

Soft-necked garlic (FooDB: FOOD00850)

Process

Not Available

Role

Biological role

Anti bacterial (HMDB: HMDB0304823)

Industrial application

Pharmaceutical industry

Antimicrobial agent

Gram(+)icide (HMDB: HMDB0304823)

Agriculture

Pesticide (HMDB: HMDB0304823)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	2.47	ALOGPS
logP	-0.52	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	-0.064	ChemAxon
pKa (Strongest Basic)	13.21	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	44.08 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	67.13 m³·mol⁻¹	ChemAxon
Polarizability	22.05 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	143.705	32859911
AllCCS	[M+H-H2O]+	139.931	32859911
AllCCS	[M+Na]+	148.224	32859911
AllCCS	[M+NH4]+	147.214	32859911
AllCCS	[M-H]-	150.143	32859911
AllCCS	[M+Na-2H]-	151.444	32859911
AllCCS	[M+HCOO]-	152.955	32859911
DeepCCS	[M+H]+	143.374	30932474
DeepCCS	[M-H]-	140.978	30932474
DeepCCS	[M-2H]-	175.706	30932474
DeepCCS	[M+Na]+	150.147	30932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Lysozyme,2TMS,isomer #1	C[Si](C)(C)N=C(CCCC[C@@H]1CCSS1)O[Si](C)(C)C	2220.4	Semi standard non polar	33892256
Lysozyme,2TMS,isomer #1	C[Si](C)(C)N=C(CCCC[C@@H]1CCSS1)O[Si](C)(C)C	2058.9	Standard non polar	33892256
Lysozyme,2TMS,isomer #1	C[Si](C)(C)N=C(CCCC[C@@H]1CCSS1)O[Si](C)(C)C	2981.5	Standard polar	33892256
Lysozyme,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N=C(CCCC[C@@H]1CCSS1)O[Si](C)(C)C(C)(C)C	2619.0	Semi standard non polar	33892256
Lysozyme,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N=C(CCCC[C@@H]1CCSS1)O[Si](C)(C)C(C)(C)C	2450.1	Standard non polar	33892256
Lysozyme,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N=C(CCCC[C@@H]1CCSS1)O[Si](C)(C)C(C)(C)C	2882.7	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 10V, Positive-QTOF	splash10-0a4r-0940000000-d79e1aa52057e567d71f	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 20V, Positive-QTOF	splash10-052r-3900000000-abd8148048c5f282d889	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 40V, Positive-QTOF	splash10-0adr-9500000000-9769c619660ab6af46d2	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 10V, Negative-QTOF	splash10-0zml-1920000000-79d57d488cb8fbc804a3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 20V, Negative-QTOF	splash10-0fdo-4910000000-d264eaf6e242c36bc563	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 40V, Negative-QTOF	splash10-0006-9000000000-289d2f20046f7819a7ca	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 10V, Positive-QTOF	splash10-0a4i-0690000000-db32b4efef6d4d06e799	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 20V, Positive-QTOF	splash10-03di-1900000000-c09c2f759aca294a35f0	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 40V, Positive-QTOF	splash10-0ika-5900000000-b388d7bb80b06afcd3b9	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 10V, Negative-QTOF	splash10-0udi-0090000000-026e73840b34e98efd4b	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 20V, Negative-QTOF	splash10-0zfr-9770000000-2f59ecc3f1f23cd58faa	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Lysozyme 40V, Negative-QTOF	splash10-0006-9000000000-1e1344f874294cd76bce	2021-10-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB000540

KNApSAcK ID

Not Available

Chemspider ID

5360246

KEGG Compound ID

Not Available

BioCyc ID

LIPOAMIDE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

83094

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Lysozyme (HMDB0304823)

MOL for HMDB0304823 (Lysozyme)

3D MOL for HMDB0304823 (Lysozyme)

3D SDF for HMDB0304823 (Lysozyme)

3D-SDF for HMDB0304823 (Lysozyme)

PDB for HMDB0304823 (Lysozyme)

3D PDB for HMDB0304823 (Lysozyme)

SMILES for HMDB0304823 (Lysozyme)

INCHI for HMDB0304823 (Lysozyme)

Structure for HMDB0304823 (Lysozyme)

3D Structure for HMDB0304823 (Lysozyme)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra