MiMeDB: Showing metabocard for Pradimicin-T2 (MMDBc0009309)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:52:11 UTC

Update Date

2022-08-31 06:29:52 UTC

Metabolite ID

MMDBc0009309

Metabolite Identification

Common Name

Pradimicin-T2

Description

Pradimicin-T2 belongs to the class of organic compounds known as tetracenequinones. These are polyaromatic hydrocarbon derivatives containing a tetracyclic cycle made up of four linearly fused benzene rings, one of which bears two ketone groups at position 1 and 4. Pradimicin-T2 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152103522D          

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M  END


  Mrv1652305152103522D          

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M  END
> <DATABASE_ID>
MMDBc0009309

> <DATABASE_NAME>
MIME

> <SMILES>
[H]C1(O)COC([H])(OC2=CC3=C(C(O)=C2)C(=O)C2=C(C(O)=C4C(=C2)[C@]([H])(O)[C@@]([H])(OC2([H])OC([H])(C)C([H])(O)C([H])(O)C2([H])O)C2=C4C(O)=C(C(O)=NCC(O)=O)C(C)=C2)C3=O)C([H])(O)C1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C37H37NO19/c1-9-3-15-22(29(48)19(9)35(53)38-7-18(41)42)21-13(27(46)34(15)57-37-33(52)31(50)24(43)10(2)55-37)6-14-23(30(21)49)26(45)12-4-11(5-16(39)20(12)25(14)44)56-36-32(51)28(47)17(40)8-54-36/h3-6,10,17,24,27-28,31-34,36-37,39-40,43,46-52H,7-8H2,1-2H3,(H,38,53)(H,41,42)/t10?,17?,24?,27-,28?,31?,32?,33?,34-,36?,37?/m0/s1

> <INCHI_KEY>
YNXJAOKAYJEVKX-PTXRADAJSA-N

> <FORMULA>
C37H37NO19

> <MOLECULAR_WEIGHT>
799.691

> <EXACT_MASS>
799.195977975

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
94

> <JCHEM_AVERAGE_POLARIZABILITY>
77.76127582794919

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-({hydroxy[(10S,11S)-2,5,11,17-tetrahydroxy-7-methyl-15,22-dioxo-10-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-19-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16(21),17,19-nonaen-6-yl]methylidene}amino)acetic acid

> <ALOGPS_LOGP>
0.57

> <JCHEM_LOGP>
1.238646166333334

> <ALOGPS_LOGS>
-2.76

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.833427576183274

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.086453581537863

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6765126347146193

> <JCHEM_POLAR_SURFACE_AREA>
343.25000000000006

> <JCHEM_REFRACTIVITY>
187.8881000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.39e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
({hydroxy[(10S,11S)-2,5,11,17-tetrahydroxy-7-methyl-15,22-dioxo-10-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-19-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16(21),17,19-nonaen-6-yl]methylidene}amino)acetic acid

> <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       9.909  -7.014   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.019  -5.946   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.060  -5.092   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.297  -7.655   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.147  -5.733   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.141  -3.384   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.539 -11.072   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -8.216  -5.946   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.430  -6.587   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.649  -4.452   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.777  -7.228   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.188  -6.587   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.621  -3.811   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.032  -4.452   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.580  -4.665   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.037  -4.665   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -9.325  -7.014   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.019 -11.499   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.320  -7.655   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.558  -5.092   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.991  -5.306   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.470  -5.733   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.401  -5.946   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.759  -3.384   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.448  -4.024   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.292  -7.014   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.731  -2.743   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -8.956  -8.509   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.840  -7.228   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.881  -6.374   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      11.389  -1.889   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -7.476  -8.936   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.909  -1.462   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.210  -3.170   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.690  -9.150   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -6.366  -7.868   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.799  -2.529   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0       9.169  -9.577   0.000  0.00  0.00           N+0
HETATM   39  O   UNK     0      -3.407  -3.170   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0     -10.805  -6.587   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      12.128 -10.431   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      11.389 -12.994   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      13.238  -3.811   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -0.818  -2.529   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0       0.662  -8.509   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0       4.361  -1.248   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0     -10.065  -9.577   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0       4.731  -8.296   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       3.251  -7.868   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      12.498  -0.821   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -7.106 -10.431   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       9.539   0.033   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       6.580 -10.218   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      -6.736  -6.374   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       9.169  -4.024   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      -4.887  -8.296   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       7.320  -2.102   0.000  0.00  0.00           O+0
HETATM   58  H   UNK     0      12.128  -4.879   0.000  0.00  0.00           H+0
HETATM   59  H   UNK     0     -10.435  -8.082   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0      12.868  -2.316   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0       5.840  -1.675   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0      -7.846  -7.441   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0      10.279  -2.957   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0      -8.586 -10.004   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0      11.019  -0.394   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0       7.690  -3.597   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0      -5.996  -9.363   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0       8.430  -1.035   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3    9   15                                                       
CONECT    4   11   12                                                       
CONECT    5   11   16                                                       
CONECT    6   13   14                                                       
CONECT    7   18   38                                                       
CONECT    8   17   54                                                       
CONECT    9    1    3   19                                                  
CONECT   10    2   24   55   58                                             
CONECT   11    4    5   56                                                  
CONECT   12    4   20   26                                                  
CONECT   13    6   21   27                                                  
CONECT   14    6   23   25                                                  
CONECT   15    3   22   34                                                  
CONECT   16    5   20   39                                                  
CONECT   17    8   28   40   59                                             
CONECT   18    7   41   42                                                  
CONECT   19    9   29   35                                                  
CONECT   20   12   16   25                                                  
CONECT   21   13   22   30                                                  
CONECT   22   15   21   29                                                  
CONECT   23   14   26   30                                                  
CONECT   24   10   31   43   60                                             
CONECT   25   14   20   44                                                  
CONECT   26   12   23   45                                                  
CONECT   27   13   34   46   61                                             
CONECT   28   17   32   47   62                                             
CONECT   29   19   22   48                                                  
CONECT   30   21   23   49                                                  
CONECT   31   24   33   50   63                                             
CONECT   32   28   36   51   64                                             
CONECT   33   31   37   52   65                                             
CONECT   34   15   27   57   66                                             
CONECT   35   19   38   53                                                  
CONECT   36   32   54   56   67                                             
CONECT   37   33   55   57   68                                             
CONECT   38    7   35                                                       
CONECT   39   16                                                            
CONECT   40   17                                                            
CONECT   41   18                                                            
CONECT   42   18                                                            
CONECT   43   24                                                            
CONECT   44   25                                                            
CONECT   45   26                                                            
CONECT   46   27                                                            
CONECT   47   28                                                            
CONECT   48   29                                                            
CONECT   49   30                                                            
CONECT   50   31                                                            
CONECT   51   32                                                            
CONECT   52   33                                                            
CONECT   53   35                                                            
CONECT   54    8   36                                                       
CONECT   55   10   37                                                       
CONECT   56   11   36                                                       
CONECT   57   34   37                                                       
CONECT   58   10                                                            
CONECT   59   17                                                            
CONECT   60   24                                                            
CONECT   61   27                                                            
CONECT   62   28                                                            
CONECT   63   31                                                            
CONECT   64   32                                                            
CONECT   65   33                                                            
CONECT   66   34                                                            
CONECT   67   36                                                            
CONECT   68   37                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  148    0
END

Synonyms

Not Available

Molecular Formula

C₃₇H₃₇NO₁₉

Average Mass

799.691

Monoisotopic Mass

799.195977975

IUPAC Name

2-({hydroxy[(10S,11S)-2,5,11,17-tetrahydroxy-7-methyl-15,22-dioxo-10-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-19-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16(21),17,19-nonaen-6-yl]methylidene}amino)acetic acid

Traditional Name

({hydroxy[(10S,11S)-2,5,11,17-tetrahydroxy-7-methyl-15,22-dioxo-10-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-19-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16(21),17,19-nonaen-6-yl]methylidene}amino)acetic acid

CAS Registry Number

Not Available

SMILES

[H]C1(O)COC([H])(OC2=CC3=C(C(O)=C2)C(=O)C2=C(C(O)=C4C(=C2)[C@]([H])(O)[C@@]([H])(OC2([H])OC([H])(C)C([H])(O)C([H])(O)C2([H])O)C2=C4C(O)=C(C(O)=NCC(O)=O)C(C)=C2)C3=O)C([H])(O)C1([H])O

InChI Identifier

InChI=1S/C37H37NO19/c1-9-3-15-22(29(48)19(9)35(53)38-7-18(41)42)21-13(27(46)34(15)57-37-33(52)31(50)24(43)10(2)55-37)6-14-23(30(21)49)26(45)12-4-11(5-16(39)20(12)25(14)44)56-36-32(51)28(47)17(40)8-54-36/h3-6,10,17,24,27-28,31-34,36-37,39-40,43,46-52H,7-8H2,1-2H3,(H,38,53)(H,41,42)/t10?,17?,24?,27-,28?,31?,32?,33?,34-,36?,37?/m0/s1

InChI Key

YNXJAOKAYJEVKX-PTXRADAJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetracenequinones. These are polyaromatic hydrocarbon derivatives containing a tetracyclic cycle made up of four linearly fused benzene rings, one of which bears two ketone groups at position 1 and 4.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Alternative Parents

Substituents

Tetracenequinone
1,4-anthraquinone
9,10-anthraquinone
Phenolic glycoside
Anthracene
Phenanthrene
N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
2-naphthalenecarboxamide
2-naphthalenecarboxylic acid or derivatives
Glycosyl compound
O-glycosyl compound
1-naphthol
Salicylic acid or derivatives
Alpha-amino acid or derivatives
Aryl ketone
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Monosaccharide
Oxane
Vinylogous acid
Secondary alcohol
Secondary carboxylic acid amide
Ketone
Carboxamide group
Acetal
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Polyol
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Organooxygen compound
Organonitrogen 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	1.39 g/L	ALOGPS
logP	0.57	ALOGPS
logP	1.24	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	3.09	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	20	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	343.25 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	187.89 m³·mol⁻¹	ChemAxon
Polarizability	77.76 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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
Bacteria	Actinobacteria	1	Human ; Human feces; Human saliva; Human urine; Human supragingival plaque; Human sputum; Human subgingival plaque	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

78445151

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139585555

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 Pradimicin-T2 (MMDBc0009309)

MOL for #<Metabolite:0x00007fa508412ee0>

3D MOL for #<Metabolite:0x00007fa508412ee0>

3D SDF for #<Metabolite:0x00007fa508412ee0>

3D-SDF for #<Metabolite:0x00007fa508412ee0>

PDB for #<Metabolite:0x00007fa508412ee0>

3D PDB for #<Metabolite:0x00007fa508412ee0>

SMILES for #<Metabolite:0x00007fa508412ee0>

INCHI for #<Metabolite:0x00007fa508412ee0>

Structure for #<Metabolite:0x00007fa508412ee0>

3D Structure for #<Metabolite:0x00007fa508412ee0>