MiMeDB: Showing metabocard for Polanrazine B (MMDBc0008974)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:38:00 UTC

Update Date

2025-10-07 16:05:32 UTC

Metabolite ID

MMDBc0008974

Metabolite Identification

Common Name

Polanrazine B

Description

Polanrazine B is a thiodiketopiperazine alkaloid, a chemical class characterized by a diketopiperazine core with sulfur-containing functional groups. It is produced by the endophytic fungus Phaeosphaeria fuckelii, which is associated with the herbal medicine Phlomis umbrosa. In a study, this fungus was found to generate four new alkaloids, termed phaeosphaones A-D, alongside four known compounds, including polanrazine B. The unique structural features of these alkaloids, particularly the β-(oxy)thiotryptophan motif, suggest potential biological activities that warrant further investigation. The presence of polanrazine B in this context highlights the diverse chemical repertoire of endophytic fungi and their potential contributions to the pharmacological properties of their host plants. As research continues, understanding the biosynthetic pathways and biological effects of polanrazine B may reveal insights into its potential therapeutic applications. (PMID:32342692 )

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152103382D          

 25 27  0  0  1  0            999 V2000
   -2.7391    1.1156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4420   -0.2822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1221   -1.5157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1812    2.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1870    0.5025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6228   -0.5378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6804    1.1112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3801    0.6740    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0480    0.7239    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3513   -0.1505    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5940   -1.3623    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7092    1.9357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3859   -0.8656    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6891    1.4389    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
 11  1  1  0  0  0  0
 11  2  1  0  0  0  0
 12  9  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  2  0  0  0  0
 13 12  1  0  0  0  0
 14  8  2  0  0  0  0
 14 13  1  0  0  0  0
 17  9  1  1  0  0  0
 17 15  1  0  0  0  0
 18 11  1  1  0  0  0
 18 16  1  0  0  0  0
 19 10  1  0  0  0  0
 19 14  1  0  0  0  0
 20 16  2  0  0  0  0
 20 17  1  0  0  0  0
 21 15  2  0  0  0  0
 21 18  1  0  0  0  0
 22 15  1  0  0  0  0
 23 16  1  0  0  0  0
 24  3  1  0  0  0  0
 17 24  1  6  0  0  0
 25  4  1  0  0  0  0
 18 25  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0008974

> <DATABASE_NAME>
MIME

> <SMILES>
CS[C@@]1(CC2=CNC3=CC=CC=C23)N=C(O)[C@@](SC)(N=C1O)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C18H23N3O2S2/c1-11(2)18(25-4)16(23)20-17(24-3,15(22)21-18)9-12-10-19-14-8-6-5-7-13(12)14/h5-8,10-11,19H,9H2,1-4H3,(H,20,23)(H,21,22)/t17-,18-/m1/s1

> <INCHI_KEY>
JXDWMFMAEDSXNI-QZTJIDSGSA-N

> <FORMULA>
C18H23N3O2S2

> <MOLECULAR_WEIGHT>
377.52

> <EXACT_MASS>
377.123169341

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
38.801464740757226

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,6R)-3-[(1H-indol-3-yl)methyl]-3,6-bis(methylsulfanyl)-6-(propan-2-yl)-3,6-dihydropyrazine-2,5-diol

> <ALOGPS_LOGP>
2.86

> <JCHEM_LOGP>
5.652357349000001

> <ALOGPS_LOGS>
-4.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.7114122833361556

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.802877063989075

> <JCHEM_PKA_STRONGEST_BASIC>
0.8174616049255272

> <JCHEM_POLAR_SURFACE_AREA>
80.97

> <JCHEM_REFRACTIVITY>
105.1457

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.79e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,6R)-3-(1H-indol-3-ylmethyl)-6-isopropyl-3,6-bis(methylsulfanyl)pyrazine-2,5-diol

> <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      -5.113   2.082   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.558  -0.527   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.228  -2.829   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.205   3.900   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.082   0.938   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.163  -1.004   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.270   2.074   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.576   1.258   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       0.090   1.351   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      -2.522  -0.281   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0      -1.109  -2.543   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -1.324   3.613   0.000  0.00  0.00           O+0
HETATM   24  S   UNK     0       0.720  -1.616   0.000  0.00  0.00           S+0
HETATM   25  S   UNK     0      -3.153   2.686   0.000  0.00  0.00           S+0
CONECT    1   11                                                            
CONECT    2   11                                                            
CONECT    3   24                                                            
CONECT    4   25                                                            
CONECT    5    6    7                                                       
CONECT    6    5    8                                                       
CONECT    7    5   13                                                       
CONECT    8    6   14                                                       
CONECT    9   12   17                                                       
CONECT   10   12   19                                                       
CONECT   11    1    2   18                                                  
CONECT   12    9   10   13                                                  
CONECT   13    7   12   14                                                  
CONECT   14    8   13   19                                                  
CONECT   15   17   21   22                                                  
CONECT   16   18   20   23                                                  
CONECT   17    9   15   20   24                                             
CONECT   18   11   16   21   25                                             
CONECT   19   10   14                                                       
CONECT   20   16   17                                                       
CONECT   21   15   18                                                       
CONECT   22   15                                                            
CONECT   23   16                                                            
CONECT   24    3   17                                                       
CONECT   25    4   18                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

Synonyms

Not Available

Molecular Formula

C₁₈H₂₃N₃O₂S₂

Average Mass

377.52

Monoisotopic Mass

377.123169341

IUPAC Name

(3R,6R)-3-[(1H-indol-3-yl)methyl]-3,6-bis(methylsulfanyl)-6-(propan-2-yl)-3,6-dihydropyrazine-2,5-diol

Traditional Name

(3R,6R)-3-(1H-indol-3-ylmethyl)-6-isopropyl-3,6-bis(methylsulfanyl)pyrazine-2,5-diol

CAS Registry Number

Not Available

SMILES

CS[C@@]1(CC2=CNC3=CC=CC=C23)N=C(O)[C@@](SC)(N=C1O)C(C)C

InChI Identifier

InChI=1S/C18H23N3O2S2/c1-11(2)18(25-4)16(23)20-17(24-3,15(22)21-18)9-12-10-19-14-8-6-5-7-13(12)14/h5-8,10-11,19H,9H2,1-4H3,(H,20,23)(H,21,22)/t17-,18-/m1/s1

InChI Key

JXDWMFMAEDSXNI-QZTJIDSGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
3-alkylindole
Indole
Indole or derivatives
Thiodioxopiperazine
Dioxopiperazine
2,5-dioxopiperazine
1,4-diazinane
Piperazine
Substituted pyrrole
Benzenoid
Heteroaromatic compound
Pyrrole
Carboxamide group
Lactam
Secondary carboxylic acid amide
Dialkylthioether
Organoheterocyclic compound
Azacycle
Sulfenyl compound
Thioether
Hemithioaminal
Carbonyl group
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0088 g/L	ALOGPS
logP	2.86	ALOGPS
logP	5.65	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	2.8	ChemAxon
pKa (Strongest Basic)	0.82	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	80.97 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	105.15 m³·mol⁻¹	ChemAxon
Polarizability	38.8 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum

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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

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

552362

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

636615

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

JXDWMFMAEDSXNI-QZTJIDSGSA-N

References

Synthesis Reference

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 Polanrazine B (MMDBc0008974)

MOL for #<Metabolite:0x00007f2ad1e40e28>

3D MOL for #<Metabolite:0x00007f2ad1e40e28>

3D SDF for #<Metabolite:0x00007f2ad1e40e28>

3D-SDF for #<Metabolite:0x00007f2ad1e40e28>

PDB for #<Metabolite:0x00007f2ad1e40e28>

3D PDB for #<Metabolite:0x00007f2ad1e40e28>

SMILES for #<Metabolite:0x00007f2ad1e40e28>

INCHI for #<Metabolite:0x00007f2ad1e40e28>

Structure for #<Metabolite:0x00007f2ad1e40e28>

3D Structure for #<Metabolite:0x00007f2ad1e40e28>