MiMeDB: Showing metabocard for Ravynic acid (MMDBc0017804)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:06:33 UTC

Update Date

2025-10-07 16:06:44 UTC

Metabolite ID

MMDBc0017804

Metabolite Identification

Common Name

Ravynic acid

Description

Ravynic acid is a polyeneyne tetramic acid, belonging to the class of antibiotic metabolites. Its chemical structure features a complex arrangement of conjugated double bonds and a tetramic acid moiety, which contributes to its biological activity. Isolated from a Penicillium species, ravynic acid exhibits notable antibiotic properties, making it a subject of interest in the study of natural products and their potential therapeutic applications (PMID:27519121 ). In terms of biochemical pathways, ravynic acid is involved in the synthesis of various secondary metabolites and may interact with cellular processes that influence microbial growth and resistance. The unique structural characteristics of ravynic acid suggest potential mechanisms of action that could disrupt bacterial cell functions, although specific pathways remain to be fully elucidated. Further research into its biosynthesis and interactions could provide insights into its role within the broader context of microbial ecology and antibiotic development.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152110062D          

 24 24  0  0  0  0            999 V2000
   -1.4719    7.0851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7966    3.0081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3004    6.2782    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9135    5.7261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7419    4.9192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5704    4.1122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3989    3.3052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.9462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0120    2.7532    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5157    6.0232    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6981    5.9811    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6143    3.0503    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4535    1.3942    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4427    2.2433    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  2  0  0  0  0
  5  4  1  0  0  0  0
  6  5  3  0  0  0  0
  7  6  1  0  0  0  0
  9  8  2  0  0  0  0
 11  2  1  0  0  0  0
 11  7  2  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 12  2  0  0  0  0
 14 13  1  0  0  0  0
 15 14  1  0  0  0  0
 16 10  1  0  0  0  0
 16 15  2  0  0  0  0
 17 12  1  0  0  0  0
 18 13  2  0  0  0  0
 19 15  1  0  0  0  0
 20  3  1  0  0  0  0
 21  4  1  0  0  0  0
 22  7  1  0  0  0  0
 23  8  1  0  0  0  0
 24  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017804

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(C)=C(\[H])C#C\C([H])=C(/C)\C(\[H])=C(/[H])\C(\O)=C1\C(O)=NCC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H15NO3/c1-3-4-5-6-7-11(2)8-9-12(17)14-13(18)10-16-15(14)19/h3-4,7-9,17H,10H2,1-2H3,(H,16,19)/b4-3+,9-8+,11-7+,14-12-

> <INCHI_KEY>
MZQBXEHXRQQBQP-NRHHSCOKSA-N

> <FORMULA>
C15H15NO3

> <MOLECULAR_WEIGHT>
257.289

> <EXACT_MASS>
257.105193347

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
28.13994532751161

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4E)-5-hydroxy-4-[(2E,4E,8E)-1-hydroxy-4-methyldeca-2,4,8-trien-6-yn-1-ylidene]-3,4-dihydro-2H-pyrrol-3-one

> <ALOGPS_LOGP>
2.31

> <JCHEM_LOGP>
2.4021228873333333

> <ALOGPS_LOGS>
-4.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.55284511288881

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.861207624103949

> <JCHEM_PKA_STRONGEST_BASIC>
1.0895989270230502

> <JCHEM_POLAR_SURFACE_AREA>
69.89

> <JCHEM_REFRACTIVITY>
78.9653

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4E)-5-hydroxy-4-[(2E,4E,8E)-1-hydroxy-4-methyldeca-2,4,8-trien-6-yn-1-ylidene]-2H-pyrrol-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -2.748  13.226   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.220   5.615   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.427  11.719   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.572  10.689   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.252   9.182   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.931   7.676   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.611   6.170   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.436   3.633   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.971   3.157   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.756   5.139   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -2.795   0.620   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0      -0.963  11.243   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0      -5.036  11.165   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      -1.147   5.694   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -4.580   2.602   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.826   4.188   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2   11                                                            
CONECT    3    1    4   20                                                  
CONECT    4    3    5   21                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6   11   22                                                  
CONECT    8    9   11   23                                                  
CONECT    9    8   12   24                                                  
CONECT   10   13   16                                                       
CONECT   11    2    7    8                                                  
CONECT   12    9   14   17                                                  
CONECT   13   10   14   18                                                  
CONECT   14   12   13   15                                                  
CONECT   15   14   16   19                                                  
CONECT   16   10   15                                                       
CONECT   17   12                                                            
CONECT   18   13                                                            
CONECT   19   15                                                            
CONECT   20    3                                                            
CONECT   21    4                                                            
CONECT   22    7                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

Synonyms

Value	Source
Ravynate	Generator

Molecular Formula

C₁₅H₁₅NO₃

Average Mass

257.289

Monoisotopic Mass

257.105193347

IUPAC Name

(4E)-5-hydroxy-4-[(2E,4E,8E)-1-hydroxy-4-methyldeca-2,4,8-trien-6-yn-1-ylidene]-3,4-dihydro-2H-pyrrol-3-one

Traditional Name

(4E)-5-hydroxy-4-[(2E,4E,8E)-1-hydroxy-4-methyldeca-2,4,8-trien-6-yn-1-ylidene]-2H-pyrrol-3-one

CAS Registry Number

Not Available

SMILES

[H]\C(C)=C(\[H])C#C\C([H])=C(/C)\C(\[H])=C(/[H])\C(\O)=C1\C(O)=NCC1=O

InChI Identifier

InChI=1S/C15H15NO3/c1-3-4-5-6-7-11(2)8-9-12(17)14-13(18)10-16-15(14)19/h3-4,7-9,17H,10H2,1-2H3,(H,16,19)/b4-3+,9-8+,11-7+,14-12-

InChI Key

MZQBXEHXRQQBQP-NRHHSCOKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolines. Pyrrolines are compounds containing a pyrroline ring, which is a five-member unsaturated aliphatic ring with one nitrogen atom and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolines

Sub Class

Not Available

Direct Parent

Pyrrolines

Alternative Parents

Substituents

Vinylogous acid
Cyclic carboximidic acid
Pyrroline
Cyclic ketone
Lactim
Ketone
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Enol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.015 g/L	ALOGPS
logP	2.31	ALOGPS
logP	2.4	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	3.86	ChemAxon
pKa (Strongest Basic)	1.09	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	69.89 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	78.97 m³·mol⁻¹	ChemAxon
Polarizability	28.14 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (void)	2025-10-23	141.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	26.2
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	473.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	419.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	521.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	315.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2171.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	70.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	508.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	450.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	255.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	206.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	134.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	7.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	327.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	115.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	392.5
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1194.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1106.2

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Ravynic acid_TMS_1	C/C=C/C#C/C=C(C)/C=C/C(O[Si](C)(C)C)=C1\C(=O)CN=C1O	standard non polar	2025-10-23	1660.55
Gas Chromatography	Ravynic acid_TMS_2	C/C=C/C#C/C=C(C)/C=C/C(O)=C1\C(=O)CN=C1O[Si](C)(C)C	standard non polar	2025-10-23	1763.32
Gas Chromatography	Ravynic acid_TMS_3	C/C=C/C#C/C=C(C)/C=C/C(O)=C1\C(O[Si](C)(C)C)=CN=C1O	standard non polar	2025-10-23	1966.94
Gas Chromatography	Ravynic acid_TMS_4	C/C=C/C#C/C=C(C)/C=C/C(O[Si](C)(C)C)=C1\C(=O)CN=C1O[Si](C)(C)C	standard non polar	2025-10-23	1999.12
Gas Chromatography	Ravynic acid_TMS_5	C/C=C/C#C/C=C(C)/C=C/C(O[Si](C)(C)C)=C1\C(O[Si](C)(C)C)=CN=C1O	standard non polar	2025-10-23	1785.4
Gas Chromatography	Ravynic acid_TMS_6	C/C=C/C#C/C=C(C)/C=C/C(O)=C1\C(O[Si](C)(C)C)=CN=C1O[Si](C)(C)C	standard non polar	2025-10-23	2165.99
Gas Chromatography	Ravynic acid_TMS_7	C/C=C/C#C/C=C(C)/C=C/C(O[Si](C)(C)C)=C1\C(O[Si](C)(C)C)=CN=C1O[Si](C)(C)C	standard non polar	2025-10-23	2208.96
Gas Chromatography	Ravynic acid_TMS_1	C/C=C/C#C/C=C(C)/C=C/C(O[Si](C)(C)C)=C1\C(=O)CN=C1O	standard polar	2025-10-23	2289.6
Gas Chromatography	Ravynic acid_TMS_2	C/C=C/C#C/C=C(C)/C=C/C(O)=C1\C(=O)CN=C1O[Si](C)(C)C	standard polar	2025-10-23	2645.75
Gas Chromatography	Ravynic acid_TMS_3	C/C=C/C#C/C=C(C)/C=C/C(O)=C1\C(O[Si](C)(C)C)=CN=C1O	standard polar	2025-10-23	2255.79
Gas Chromatography	Ravynic acid_TMS_4	C/C=C/C#C/C=C(C)/C=C/C(O[Si](C)(C)C)=C1\C(=O)CN=C1O[Si](C)(C)C	standard polar	2025-10-23	1426.08
Gas Chromatography	Ravynic acid_TMS_5	C/C=C/C#C/C=C(C)/C=C/C(O[Si](C)(C)C)=C1\C(O[Si](C)(C)C)=CN=C1O	standard polar	2025-10-23	1374.97
Gas Chromatography	Ravynic acid_TMS_6	C/C=C/C#C/C=C(C)/C=C/C(O)=C1\C(O[Si](C)(C)C)=CN=C1O[Si](C)(C)C	standard polar	2025-10-23	1616.01
Gas Chromatography	Ravynic acid_TMS_7	C/C=C/C#C/C=C(C)/C=C/C(O[Si](C)(C)C)=C1\C(O[Si](C)(C)C)=CN=C1O[Si](C)(C)C	standard polar	2025-10-23	2861.79

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78435371

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

132596093

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Ravynic acid (MMDBc0017804)

MOL for #<Metabolite:0x00007f9ad0f750b8>

3D MOL for #<Metabolite:0x00007f9ad0f750b8>

3D SDF for #<Metabolite:0x00007f9ad0f750b8>

3D-SDF for #<Metabolite:0x00007f9ad0f750b8>

PDB for #<Metabolite:0x00007f9ad0f750b8>

3D PDB for #<Metabolite:0x00007f9ad0f750b8>

SMILES for #<Metabolite:0x00007f9ad0f750b8>

INCHI for #<Metabolite:0x00007f9ad0f750b8>

Structure for #<Metabolite:0x00007f9ad0f750b8>

3D Structure for #<Metabolite:0x00007f9ad0f750b8>