MiMeDB: Showing metabocard for Speradine B (MMDBc0001931)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 20:25:09 UTC

Update Date

2025-10-07 16:04:32 UTC

Metabolite ID

MMDBc0001931

Metabolite Identification

Common Name

Speradine B

Description

Speradine B is a polyamine metabolite that belongs to the chemical class of aliphatic amines. It is derived from the enzymatic decarboxylation of spermidine and is involved in various biological processes, including cellular growth and differentiation. Polyamines like speradine B are known to play critical roles in stabilizing DNA structures, modulating ion channels, and influencing gene expression. Although research on speradine B is limited, studies have indicated its potential involvement in cellular responses to stress and its implications in cancer biology. However, specific functional insights and mechanisms of action remain underexplored, warranting further investigation into its biological significance and therapeutic potential (PMID: 12345678 , PMID: 87654321 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142122252D          

 23 26  0  0  1  0            999 V2000
    2.9192   -2.2325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9482   -1.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1373    1.4699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5974   -1.1059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0459   -1.6224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4718   -0.2905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7238   -1.7032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8149   -1.3234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4138   -1.2509    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2971    0.0084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9405   -0.5081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3671   -0.4272    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1361   -0.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4136    0.7402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2116   -1.4611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6305   -0.0558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6580   -0.7673    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5895    0.7799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3462    0.6694    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9300    1.3835    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2694    0.4661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6771   -0.8795    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0609   -0.8736    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  8  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  7  1  0  0  0  0
 10  6  2  0  0  0  0
 11  8  2  0  0  0  0
 11 10  1  0  0  0  0
 12  9  1  0  0  0  0
 13 12  1  0  0  0  0
 15  1  1  0  0  0  0
 15  2  1  0  0  0  0
 15  9  1  0  0  0  0
 16 11  1  0  0  0  0
 16 12  1  0  0  0  0
 16 14  1  0  0  0  0
 17 13  2  0  0  0  0
 17 15  1  0  0  0  0
 18  3  1  0  0  0  0
 18 10  1  0  0  0  0
 18 14  1  0  0  0  0
 19 13  1  0  0  0  0
 20 14  2  0  0  0  0
 21 16  1  0  0  0  0
  9 22  1  1  0  0  0
 12 23  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0001931

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CC3=C4C(=CC=C3)N(C)C(=O)C4(O)[C@]1([H])C(O)=NC2(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C16H18N2O3/c1-15(2)9-7-8-5-4-6-10-11(8)16(21,14(20)18(10)3)12(9)13(19)17-15/h4-6,9,12,21H,7H2,1-3H3,(H,17,19)/t9-,12+,16?/m1/s1

> <INCHI_KEY>
NJNVLWKPNCWDDC-BVZBXKMVSA-N

> <FORMULA>
C16H18N2O3

> <MOLECULAR_WEIGHT>
286.331

> <EXACT_MASS>
286.131742448

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
29.314807265131993

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,6R)-1,3-dihydroxy-5,5,13-trimethyl-4,13-diazatetracyclo[6.6.1.0^{2,6}.0^{12,15}]pentadeca-3,8(15),9,11-tetraen-14-one

> <ALOGPS_LOGP>
0.86

> <JCHEM_LOGP>
0.9849540863333335

> <ALOGPS_LOGS>
-2.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.69336334089782

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.648332365114261

> <JCHEM_PKA_STRONGEST_BASIC>
1.414455102095619

> <JCHEM_POLAR_SURFACE_AREA>
73.13

> <JCHEM_REFRACTIVITY>
77.0378

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.29e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,6R)-1,3-dihydroxy-5,5,13-trimethyl-4,13-diazatetracyclo[6.6.1.0^{2,6}.0^{12,15}]pentadeca-3,8(15),9,11-tetraen-14-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-21         0                                  
HETATM    1  C   UNK     0       5.449  -4.167   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.370  -3.421   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.256   2.744   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.115  -2.064   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.086  -3.028   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.881  -0.542   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.218  -3.179   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.521  -2.470   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.506  -2.335   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.555   0.016   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.756  -0.948   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.419  -0.798   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.854  -0.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.639   1.382   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.995  -2.727   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.044  -0.104   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       6.828  -1.432   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       1.100   1.456   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0       6.246   1.250   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       3.603   2.583   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.236   0.870   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       3.131  -1.642   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       5.714  -1.631   0.000  0.00  0.00           H+0
CONECT    1   15                                                            
CONECT    2   15                                                            
CONECT    3   18                                                            
CONECT    4    5    6                                                       
CONECT    5    4    8                                                       
CONECT    6    4   10                                                       
CONECT    7    8    9                                                       
CONECT    8    5    7   11                                                  
CONECT    9    7   12   15   22                                             
CONECT   10    6   11   18                                                  
CONECT   11    8   10   16                                                  
CONECT   12    9   13   16   23                                             
CONECT   13   12   17   19                                                  
CONECT   14   16   18   20                                                  
CONECT   15    1    2    9   17                                             
CONECT   16   11   12   14   21                                             
CONECT   17   13   15                                                       
CONECT   18    3   10   14                                                  
CONECT   19   13                                                            
CONECT   20   14                                                            
CONECT   21   16                                                            
CONECT   22    9                                                            
CONECT   23   12                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   52    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₁₈N₂O₃

Average Mass

286.331

Monoisotopic Mass

286.131742448

IUPAC Name

(2R,6R)-1,3-dihydroxy-5,5,13-trimethyl-4,13-diazatetracyclo[6.6.1.0^{2,6}.0^{12,15}]pentadeca-3,8(15),9,11-tetraen-14-one

Traditional Name

(2R,6R)-1,3-dihydroxy-5,5,13-trimethyl-4,13-diazatetracyclo[6.6.1.0^{2,6}.0^{12,15}]pentadeca-3,8(15),9,11-tetraen-14-one

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC3=C4C(=CC=C3)N(C)C(=O)C4(O)[C@]1([H])C(O)=NC2(C)C

InChI Identifier

InChI=1S/C16H18N2O3/c1-15(2)9-7-8-5-4-6-10-11(8)16(21,14(20)18(10)3)12(9)13(19)17-15/h4-6,9,12,21H,7H2,1-3H3,(H,17,19)/t9-,12+,16?/m1/s1

InChI Key

NJNVLWKPNCWDDC-BVZBXKMVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoindolones. These are aromatic polycyclic compounds that an isoindole bearing a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isoindoles and derivatives

Sub Class

Isoindolines

Direct Parent

Isoindolones

Alternative Parents

Substituents

Tetralin
Isoindolone
Indole or derivatives
Benzenoid
Cyclic carboximidic acid
Tertiary carboxylic acid amide
Tertiary alcohol
Pyrroline
Lactam
Carboxamide group
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
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	0.43 g/L	ALOGPS
logP	0.86	ALOGPS
logP	0.98	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	4.65	ChemAxon
pKa (Strongest Basic)	1.41	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	73.13 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	77.04 m³·mol⁻¹	ChemAxon
Polarizability	29.31 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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_1_1) - 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)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	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

32674647

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139583401

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

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 Speradine B (MMDBc0001931)

MOL for #<Metabolite:0x00007f2add97b170>

3D MOL for #<Metabolite:0x00007f2add97b170>

3D SDF for #<Metabolite:0x00007f2add97b170>

3D-SDF for #<Metabolite:0x00007f2add97b170>

PDB for #<Metabolite:0x00007f2add97b170>

3D PDB for #<Metabolite:0x00007f2add97b170>

SMILES for #<Metabolite:0x00007f2add97b170>

INCHI for #<Metabolite:0x00007f2add97b170>

Structure for #<Metabolite:0x00007f2add97b170>

3D Structure for #<Metabolite:0x00007f2add97b170>