MiMeDB: Showing metabocard for Zafrin (MMDBc0015338)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:11:05 UTC

Update Date

2025-10-07 16:06:24 UTC

Metabolite ID

MMDBc0015338

Metabolite Identification

Common Name

Zafrin

Description

Zafrin is a novel metabolite classified as a phenanthrenone, specifically identified as 4beta-methyl-5,6,7,8-tetrahydro-1(4beta-H)-phenanthrenone. It was isolated from a crude extract of the marine bacterium Pseudomonas stutzeri (PMID:18093138 ). This compound exhibits significant antibacterial properties, demonstrating strong activity against both Gram-positive and Gram-negative bacteria, including human pathogens such as Staphylococcus aureus and Salmonella typhi (PMID:18093138 ). However, it does not inhibit the growth of eukaryotic organisms like Candida albicans and Schizosaccharomyces pombe (PMID:18093138 ). The chemical diversity of bioactive substances from marine Pseudomonas includes zafrin among other compounds such as pyroles and phenazines (PMID:19582493 ). Zafrin's potential therapeutic applications are supported by various studies highlighting its antibacterial efficacy (PMID:40892842 , PMID:39282168 , PMID:34605479 ). As research continues, zafrin may provide insights into novel antibacterial agents derived from marine sources, contributing to the understanding of microbial interactions and the development of new treatments against resistant bacterial strains.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152108112D          

 16 18  0  0  1  0            999 V2000
    1.2375    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3000    0.2211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  5  2  1  0  0  0  0
  6  4  1  0  0  0  0
  7  4  2  0  0  0  0
  9  8  1  0  0  0  0
 10  3  1  0  0  0  0
 11  5  1  0  0  0  0
 11  8  2  0  0  0  0
 12  9  2  0  0  0  0
 13  6  2  0  0  0  0
 13 12  1  0  0  0  0
 14  7  1  0  0  0  0
 14 12  1  0  0  0  0
 15  1  1  1  0  0  0
 15 10  1  0  0  0  0
 15 11  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015338

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@]12CCCCC1=CC=C1C(=O)C=CC=C21

> <INCHI_IDENTIFIER>
InChI=1S/C15H16O/c1-15-10-3-2-5-11(15)8-9-12-13(15)6-4-7-14(12)16/h4,6-9H,2-3,5,10H2,1H3/t15-/m0/s1

> <INCHI_KEY>
AHCCSFZXRLQQHD-HNNXBMFYSA-N

> <FORMULA>
C15H16O

> <MOLECULAR_WEIGHT>
212.292

> <EXACT_MASS>
212.120115135

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.09364905721931

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4bS)-4b-methyl-1,4b,5,6,7,8-hexahydrophenanthren-1-one

> <ALOGPS_LOGP>
4.43

> <JCHEM_LOGP>
3.0801600343333337

> <ALOGPS_LOGS>
-3.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.8024977345955095

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
69.41159999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.43e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4bS)-4b-methyl-5,6,7,8-tetrahydrophenanthren-1-one

> <JCHEM_VEBER_RULE>
1

$$$$

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       2.310   4.414   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.540   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.770   4.414   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.390   4.414   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770   1.746   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.850   4.414   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.160   3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.540   0.413   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.080   0.413   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.770   4.414   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.770   1.746   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.850   1.746   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.080   3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.390   1.746   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.540   3.080   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.160   0.413   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2    3    5                                                       
CONECT    3    2   10                                                       
CONECT    4    6    7                                                       
CONECT    5    2   11                                                       
CONECT    6    4   13                                                       
CONECT    7    4   14                                                       
CONECT    8    9   11                                                       
CONECT    9    8   12                                                       
CONECT   10    3   15                                                       
CONECT   11    5    8   15                                                  
CONECT   12    9   13   14                                                  
CONECT   13    6   12   15                                                  
CONECT   14    7   12   16                                                  
CONECT   15    1   10   11   13                                             
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₁₆O

Average Mass

212.292

Monoisotopic Mass

212.120115135

IUPAC Name

(4bS)-4b-methyl-1,4b,5,6,7,8-hexahydrophenanthren-1-one

Traditional Name

(4bS)-4b-methyl-5,6,7,8-tetrahydrophenanthren-1-one

CAS Registry Number

Not Available

SMILES

C[C@]12CCCCC1=CC=C1C(=O)C=CC=C21

InChI Identifier

InChI=1S/C15H16O/c1-15-10-3-2-5-11(15)8-9-12-13(15)6-4-7-14(12)16/h4,6-9H,2-3,5,10H2,1H3/t15-/m0/s1

InChI Key

AHCCSFZXRLQQHD-HNNXBMFYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydrophenanthrenes. These are a phenanthrene derivative where at least one ring CC bond is substituted by hydrogenation.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenanthrenes and derivatives

Sub Class

Hydrophenanthrenes

Direct Parent

Hydrophenanthrenes

Alternative Parents

Substituents

Hydrophenanthrene
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.084 g/L	ALOGPS
logP	4.43	ALOGPS
logP	3.08	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	17.07 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	69.41 m³·mol⁻¹	ChemAxon
Polarizability	24.09 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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
Bacteria/Eubacteria	Proteobacteria	1	Human	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

C00003761

Chemspider ID

78440380

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139587310

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 Zafrin (MMDBc0015338)

MOL for #<Metabolite:0x00007f8de82c10c8>

3D MOL for #<Metabolite:0x00007f8de82c10c8>

3D SDF for #<Metabolite:0x00007f8de82c10c8>

3D-SDF for #<Metabolite:0x00007f8de82c10c8>

PDB for #<Metabolite:0x00007f8de82c10c8>

3D PDB for #<Metabolite:0x00007f8de82c10c8>

SMILES for #<Metabolite:0x00007f8de82c10c8>

INCHI for #<Metabolite:0x00007f8de82c10c8>

Structure for #<Metabolite:0x00007f8de82c10c8>

3D Structure for #<Metabolite:0x00007f8de82c10c8>