MiMeDB: Showing metabocard for Tubingensin A (MMDBc0013643)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 04:55:22 UTC

Update Date

2022-08-31 06:36:31 UTC

Metabolite ID

MMDBc0013643

Metabolite Identification

Common Name

Tubingensin A

Description

Tubingensin A belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene. Based on a literature review a small amount of articles have been published on Tubingensin A.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152106552D          

 32 36  0  0  1  0            999 V2000
    5.4324   -3.5936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0118   -3.4396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5262    0.1492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2809    0.4823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5994   -1.6105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1534   -0.9992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1896   -1.7992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8554   -2.2863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7930   -1.4363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9011   -0.2137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1031   -1.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7690   -1.6452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7905    1.1485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2785   -0.9790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0357    0.8154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2111    0.9945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0333   -0.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7665   -3.1065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1920   -0.3379    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4563    0.6614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5406   -0.6508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7880   -0.3128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3674   -0.1588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0946   -0.0395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8770    0.5074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5237   -1.3121    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9468   -0.0048    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6127   -0.4919    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.6845    0.6763    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7761   -2.0976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4373   -0.6710    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 12 11  1  0  0  0  0
 14  7  1  0  0  0  0
 15 13  1  0  0  0  0
 18  1  1  0  0  0  0
 18  2  1  0  0  0  0
 18  8  2  0  0  0  0
 19  3  1  1  0  0  0
 19 11  1  0  0  0  0
 20 13  1  0  0  0  0
 20 16  2  0  0  0  0
 21  9  2  0  0  0  0
 22 17  1  0  0  0  0
 22 21  1  0  0  0  0
 23 17  2  0  0  0  0
 23 20  1  0  0  0  0
 24 10  2  0  0  0  0
 24 21  1  0  0  0  0
 25 16  1  0  0  0  0
 25 22  2  0  0  0  0
 26 12  1  0  0  0  0
 27  4  1  1  0  0  0
 27 15  1  0  0  0  0
 27 19  1  0  0  0  0
 28 14  1  1  0  0  0
 28 23  1  0  0  0  0
 28 26  1  0  0  0  0
 28 27  1  0  0  0  0
 29 24  1  0  0  0  0
 29 25  1  0  0  0  0
 26 30  1  6  0  0  0
 19 31  1  6  0  0  0
 26 32  1  6  0  0  0
M  END


  Mrv1652305152106552D          

 32 36  0  0  1  0            999 V2000
    5.4324   -3.5936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0118   -3.4396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5262    0.1492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2809    0.4823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5994   -1.6105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1534   -0.9992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1896   -1.7992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8554   -2.2863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7930   -1.4363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9011   -0.2137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1031   -1.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7690   -1.6452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7905    1.1485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2785   -0.9790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0357    0.8154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2111    0.9945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0333   -0.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7665   -3.1065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1920   -0.3379    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4563    0.6614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5406   -0.6508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7880   -0.3128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3674   -0.1588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0946   -0.0395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8770    0.5074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5237   -1.3121    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9468   -0.0048    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6127   -0.4919    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.6845    0.6763    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7761   -2.0976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4373   -0.6710    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 12 11  1  0  0  0  0
 14  7  1  0  0  0  0
 15 13  1  0  0  0  0
 18  1  1  0  0  0  0
 18  2  1  0  0  0  0
 18  8  2  0  0  0  0
 19  3  1  1  0  0  0
 19 11  1  0  0  0  0
 20 13  1  0  0  0  0
 20 16  2  0  0  0  0
 21  9  2  0  0  0  0
 22 17  1  0  0  0  0
 22 21  1  0  0  0  0
 23 17  2  0  0  0  0
 23 20  1  0  0  0  0
 24 10  2  0  0  0  0
 24 21  1  0  0  0  0
 25 16  1  0  0  0  0
 25 22  2  0  0  0  0
 26 12  1  0  0  0  0
 27  4  1  1  0  0  0
 27 15  1  0  0  0  0
 27 19  1  0  0  0  0
 28 14  1  1  0  0  0
 28 23  1  0  0  0  0
 28 26  1  0  0  0  0
 28 27  1  0  0  0  0
 29 24  1  0  0  0  0
 29 25  1  0  0  0  0
 26 30  1  6  0  0  0
 19 31  1  6  0  0  0
 26 32  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0013643

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(C)CC[C@]([H])(O)[C@@]2(CCC=C(C)C)C3=CC4=C(NC5=CC=CC=C45)C=C3CC[C@@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C28H35NO/c1-18(2)8-7-14-28-23-17-22-21-9-5-6-10-24(21)29-25(22)16-20(23)13-15-27(28,4)19(3)11-12-26(28)30/h5-6,8-10,16-17,19,26,29-30H,7,11-15H2,1-4H3/t19-,26+,27+,28-/m1/s1

> <INCHI_KEY>
BWCQRIGHZTXFEA-AIERRPMVSA-N

> <FORMULA>
C28H35NO

> <MOLECULAR_WEIGHT>
401.594

> <EXACT_MASS>
401.271864751

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
48.68401192763186

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(16S,17R,20S,21R)-16,17-dimethyl-21-(4-methylpent-3-en-1-yl)-10-azapentacyclo[11.8.0.0^{3,11}.0^{4,9}.0^{16,21}]henicosa-1,3(11),4,6,8,12-hexaen-20-ol

> <ALOGPS_LOGP>
7.07

> <JCHEM_LOGP>
6.858606059666665

> <ALOGPS_LOGS>
-7.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.305958581743369

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.469407370598166

> <JCHEM_PKA_STRONGEST_BASIC>
-2.985870392946337

> <JCHEM_POLAR_SURFACE_AREA>
36.019999999999996

> <JCHEM_REFRACTIVITY>
126.26829999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.02e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(16S,17R,20S,21R)-16,17-dimethyl-21-(4-methylpent-3-en-1-yl)-10-azapentacyclo[11.8.0.0^{3,11}.0^{4,9}.0^{16,21}]henicosa-1,3(11),4,6,8,12-hexaen-20-ol

> <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      10.140  -6.708   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.489  -6.421   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.849   0.279   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.258   0.900   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.186  -3.006   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      15.220  -1.865   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.821  -3.359   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.063  -4.268   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.680  -2.681   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.749  -0.399   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.926  -2.162   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.169  -3.071   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.076   2.144   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.987  -1.827   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.667   1.522   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.727   1.856   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.395  -1.206   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.898  -5.799   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.092  -0.631   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.318   1.235   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.209  -1.215   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.804  -0.584   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.153  -0.296   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      13.243  -0.074   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.970   0.947   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.578  -2.449   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.501  -0.009   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.744  -0.918   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      12.478   1.262   0.000  0.00  0.00           N+0
HETATM   30  O   UNK     0       7.049  -3.915   0.000  0.00  0.00           O+0
HETATM   31  H   UNK     0       2.683  -1.253   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       5.335  -1.540   0.000  0.00  0.00           H+0
CONECT    1   18                                                            
CONECT    2   18                                                            
CONECT    3   19                                                            
CONECT    4   27                                                            
CONECT    5    6    9                                                       
CONECT    6    5   10                                                       
CONECT    7    8   14                                                       
CONECT    8    7   18                                                       
CONECT    9    5   21                                                       
CONECT   10    6   24                                                       
CONECT   11   12   19                                                       
CONECT   12   11   26                                                       
CONECT   13   15   20                                                       
CONECT   14    7   28                                                       
CONECT   15   13   27                                                       
CONECT   16   20   25                                                       
CONECT   17   22   23                                                       
CONECT   18    1    2    8                                                  
CONECT   19    3   11   27   31                                             
CONECT   20   13   16   23                                                  
CONECT   21    9   22   24                                                  
CONECT   22   17   21   25                                                  
CONECT   23   17   20   28                                                  
CONECT   24   10   21   29                                                  
CONECT   25   16   22   29                                                  
CONECT   26   12   28   30   32                                             
CONECT   27    4   15   19   28                                             
CONECT   28   14   23   26   27                                             
CONECT   29   24   25                                                       
CONECT   30   26                                                            
CONECT   31   19                                                            
CONECT   32   26                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   72    0
END

Synonyms

Not Available

Molecular Formula

C₂₈H₃₅NO

Average Mass

401.594

Monoisotopic Mass

401.271864751

IUPAC Name

(16S,17R,20S,21R)-16,17-dimethyl-21-(4-methylpent-3-en-1-yl)-10-azapentacyclo[11.8.0.0^{3,11}.0^{4,9}.0^{16,21}]henicosa-1,3(11),4,6,8,12-hexaen-20-ol

Traditional Name

(16S,17R,20S,21R)-16,17-dimethyl-21-(4-methylpent-3-en-1-yl)-10-azapentacyclo[11.8.0.0^{3,11}.0^{4,9}.0^{16,21}]henicosa-1,3(11),4,6,8,12-hexaen-20-ol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C)CC[C@]([H])(O)[C@@]2(CCC=C(C)C)C3=CC4=C(NC5=CC=CC=C45)C=C3CC[C@@]12C

InChI Identifier

InChI=1S/C28H35NO/c1-18(2)8-7-14-28-23-17-22-21-9-5-6-10-24(21)29-25(22)16-20(23)13-15-27(28,4)19(3)11-12-26(28)30/h5-6,8-10,16-17,19,26,29-30H,7,11-15H2,1-4H3/t19-,26+,27+,28-/m1/s1

InChI Key

BWCQRIGHZTXFEA-AIERRPMVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenanthrenes and derivatives

Sub Class

Not Available

Direct Parent

Phenanthrenes and derivatives

Alternative Parents

Substituents

Phenanthrene
Carbazole
Tetralin
Indole
Indole or derivatives
Cyclic alcohol
Pyrrole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Alcohol
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	1.0e-05 g/L	ALOGPS
logP	7.07	ALOGPS
logP	6.86	ChemAxon
logS	-7.6	ALOGPS
pKa (Strongest Acidic)	14.47	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	36.02 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	126.27 m³·mol⁻¹	ChemAxon
Polarizability	48.68 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

Metabolic Reactions

Not Available

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	2	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

10267469

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14413056

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

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 Tubingensin A (MMDBc0013643)

MOL for #<Metabolite:0x00007f47054c2338>

3D MOL for #<Metabolite:0x00007f47054c2338>

3D SDF for #<Metabolite:0x00007f47054c2338>

3D-SDF for #<Metabolite:0x00007f47054c2338>

PDB for #<Metabolite:0x00007f47054c2338>

3D PDB for #<Metabolite:0x00007f47054c2338>

SMILES for #<Metabolite:0x00007f47054c2338>

INCHI for #<Metabolite:0x00007f47054c2338>

Structure for #<Metabolite:0x00007f47054c2338>

3D Structure for #<Metabolite:0x00007f47054c2338>