MiMeDB: Showing metabocard for Benanomicin B (MMDBc0001397)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 19:37:08 UTC

Update Date

2025-10-07 16:04:28 UTC

Metabolite ID

MMDBc0001397

Metabolite Identification

Common Name

Benanomicin B

Description

Benanomicin B is a polyketide metabolite characterized by its aromatic structure. It has been identified in specific microbial strains, where one strain was noted for producing benanomicin B alongside its dexylosyl derivative, highlighting its potential biosynthetic pathways (PMID:21119678 ). The total synthesis of benanomicin B has been achieved through a regio- and stereocontrolled process, emphasizing its complex chemical architecture and the challenges associated with its synthesis (PMID:15900522 ). Additionally, significant advancements in synthetic methodologies have been documented, culminating in the first total synthesis of benanomicin B, alongside other related compounds (PMID:17907132 ). These studies not only contribute to the understanding of benanomicin B's chemical properties but also open avenues for exploring its biological activities and potential applications in pharmaceuticals.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142121372D          

 71 77  0  0  1  0            999 V2000
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M  END


  Mrv1652305142121372D          

 71 77  0  0  1  0            999 V2000
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 33 51  1  6  0  0  0
 36 52  1  4  0  0  0
 53 37  2  0  0  0  0
 54 37  1  0  0  0  0
 55  4  1  0  0  0  0
 55 13  1  0  0  0  0
 56  9  1  0  0  0  0
 56 38  1  0  0  0  0
 57 12  1  0  0  0  0
 57 39  1  0  0  0  0
 34 58  1  1  0  0  0
 39 58  1  1  0  0  0
 35 59  1  6  0  0  0
 38 59  1  1  0  0  0
 11 60  1  1  0  0  0
 12 61  1  6  0  0  0
 19 62  1  1  0  0  0
 25 63  1  6  0  0  0
 28 64  1  1  0  0  0
 29 65  1  6  0  0  0
 32 66  1  1  0  0  0
 33 67  1  1  0  0  0
 34 68  1  6  0  0  0
 35 69  1  6  0  0  0
 38 70  1  6  0  0  0
 39 71  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0001397

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(N=C(O)C1=C(O)C2=C(C=C1C)[C@]([H])(O[C@]1([H])O[C@]([H])(C)[C@]([H])(N)[C@]([H])(O[C@]3([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@@]1([H])O)[C@@]([H])(O)C1=CC3=C(C(O)=C21)C(=O)C1=C(C(O)=CC(OC)=C1)C3=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C39H42N2O18/c1-10-5-17-23(30(48)20(10)36(52)41-11(2)37(53)54)22-15(8-16-24(31(22)49)27(45)14-6-13(55-4)7-18(42)21(14)26(16)44)28(46)34(17)58-39-33(51)35(25(40)12(3)57-39)59-38-32(50)29(47)19(43)9-56-38/h5-8,11-12,19,25,28-29,32-35,38-39,42-43,46-51H,9,40H2,1-4H3,(H,41,52)(H,53,54)/t11-,12-,19-,25+,28+,29+,32-,33-,34+,35+,38+,39+/m1/s1

> <INCHI_KEY>
IHIIRQILYAXIOH-NUVDETJMSA-N

> <FORMULA>
C39H42N2O18

> <MOLECULAR_WEIGHT>
826.761

> <EXACT_MASS>
826.24326252

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
101

> <JCHEM_AVERAGE_POLARIZABILITY>
83.35064761669199

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-({[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[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](hydroxy)methylidene}amino)propanoic acid

> <ALOGPS_LOGP>
0.57

> <JCHEM_LOGP>
0.07325497972811018

> <ALOGPS_LOGS>
-3.10

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.84765673665628

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.8247370836676158

> <JCHEM_PKA_STRONGEST_BASIC>
9.244233653722322

> <JCHEM_POLAR_SURFACE_AREA>
338.04

> <JCHEM_REFRACTIVITY>
198.7907000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.51e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-({[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[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](hydroxy)methylidene}amino)propanoic acid

> <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       9.909  -7.014   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.019 -11.499   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.019  -5.946   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.366  -7.868   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.060  -5.092   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.297  -7.655   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.147  -5.733   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.141  -3.384   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.827  -3.170   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.430  -6.587   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.539 -11.072   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.649  -4.452   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.777  -7.228   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.188  -6.587   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.621  -3.811   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.032  -4.452   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.580  -4.665   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.037  -4.665   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      16.937  -2.102   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.320  -7.655   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.558  -5.092   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.991  -5.306   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.470  -5.733   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.401  -5.946   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      11.759  -3.384   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.448  -4.024   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.292  -7.014   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.731  -2.743   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      16.567  -0.607   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.840  -7.228   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.881  -6.374   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      15.088  -0.180   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      11.389  -1.889   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.690  -9.150   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.430 -12.140   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      13.978  -1.248   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       8.799  -2.529   0.000  0.00  0.00           C+0
HETATM   40  N   UNK     0      13.238  -3.811   0.000  0.00  0.00           N+0
HETATM   41  N   UNK     0       9.169  -9.577   0.000  0.00  0.00           N+0
HETATM   42  O   UNK     0      -3.407  -3.170   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      18.417  -2.529   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      17.677   0.460   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      14.718   1.315   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       9.539   0.033   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       6.580 -10.218   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       8.799 -13.635   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       6.950 -11.713   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      -4.887  -8.296   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      14.348  -2.743   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       9.169  -4.024   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0       7.320  -2.102   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      12.498  -0.821   0.000  0.00  0.00           O+0
HETATM   60  H   UNK     0       9.909 -12.567   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0      12.128  -4.879   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0      18.047  -1.035   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0      12.868  -2.316   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0       5.840  -1.675   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0      15.458  -1.675   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0      16.197   0.887   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0      11.019  -0.394   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0       7.690  -3.597   0.000  0.00  0.00           H+0
HETATM   69  H   UNK     0      10.279  -2.957   0.000  0.00  0.00           H+0
HETATM   70  H   UNK     0      13.608   0.247   0.000  0.00  0.00           H+0
HETATM   71  H   UNK     0       8.430  -1.035   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   55                                                            
CONECT    5   10   17                                                       
CONECT    6   13   14                                                       
CONECT    7   13   18                                                       
CONECT    8   15   16                                                       
CONECT    9   19   56                                                       
CONECT   10    1    5   20                                                  
CONECT   11    2   37   41   60                                             
CONECT   12    3   25   57   61                                             
CONECT   13    6    7   55                                                  
CONECT   14    6   21   27                                                  
CONECT   15    8   22   28                                                  
CONECT   16    8   24   26                                                  
CONECT   17    5   23   34                                                  
CONECT   18    7   21   42                                                  
CONECT   19    9   29   43   62                                             
CONECT   20   10   30   36                                                  
CONECT   21   14   18   26                                                  
CONECT   22   15   23   31                                                  
CONECT   23   17   22   30                                                  
CONECT   24   16   27   31                                                  
CONECT   25   12   35   40   63                                             
CONECT   26   16   21   44                                                  
CONECT   27   14   24   45                                                  
CONECT   28   15   34   46   64                                             
CONECT   29   19   32   47   65                                             
CONECT   30   20   23   48                                                  
CONECT   31   22   24   49                                                  
CONECT   32   29   38   50   66                                             
CONECT   33   35   39   51   67                                             
CONECT   34   17   28   58   68                                             
CONECT   35   25   33   59   69                                             
CONECT   36   20   41   52                                                  
CONECT   37   11   53   54                                                  
CONECT   38   32   56   59   70                                             
CONECT   39   33   57   58   71                                             
CONECT   40   25                                                            
CONECT   41   11   36                                                       
CONECT   42   18                                                            
CONECT   43   19                                                            
CONECT   44   26                                                            
CONECT   45   27                                                            
CONECT   46   28                                                            
CONECT   47   29                                                            
CONECT   48   30                                                            
CONECT   49   31                                                            
CONECT   50   32                                                            
CONECT   51   33                                                            
CONECT   52   36                                                            
CONECT   53   37                                                            
CONECT   54   37                                                            
CONECT   55    4   13                                                       
CONECT   56    9   38                                                       
CONECT   57   12   39                                                       
CONECT   58   34   39                                                       
CONECT   59   35   38                                                       
CONECT   60   11                                                            
CONECT   61   12                                                            
CONECT   62   19                                                            
CONECT   63   25                                                            
CONECT   64   28                                                            
CONECT   65   29                                                            
CONECT   66   32                                                            
CONECT   67   33                                                            
CONECT   68   34                                                            
CONECT   69   35                                                            
CONECT   70   38                                                            
CONECT   71   39                                                            
MASTER        0    0    0    0    0    0    0    0   71    0  154    0
END

Synonyms

Value	Source
Pradimicin C	MeSH
Benanomicin b	ChEBI

Molecular Formula

C₃₉H₄₂N₂O₁₈

Average Mass

826.761

Monoisotopic Mass

826.24326252

IUPAC Name

(2R)-2-({[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[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](hydroxy)methylidene}amino)propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@](C)(N=C(O)C1=C(O)C2=C(C=C1C)[C@]([H])(O[C@]1([H])O[C@]([H])(C)[C@]([H])(N)[C@]([H])(O[C@]3([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@@]1([H])O)[C@@]([H])(O)C1=CC3=C(C(O)=C21)C(=O)C1=C(C(O)=CC(OC)=C1)C3=O)C(O)=O

InChI Identifier

InChI=1S/C39H42N2O18/c1-10-5-17-23(30(48)20(10)36(52)41-11(2)37(53)54)22-15(8-16-24(31(22)49)27(45)14-6-13(55-4)7-18(42)21(14)26(16)44)28(46)34(17)58-39-33(51)35(25(40)12(3)57-39)59-38-32(50)29(47)19(43)9-56-38/h5-8,11-12,19,25,28-29,32-35,38-39,42-43,46-51H,9,40H2,1-4H3,(H,41,52)(H,53,54)/t11-,12-,19-,25+,28+,29+,32-,33-,34+,35+,38+,39+/m1/s1

InChI Key

IHIIRQILYAXIOH-NUVDETJMSA-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

Aminoglycoside core
Tetracenequinone
9,10-anthraquinone
1,4-anthraquinone
Phenanthrene
Anthracene
2-naphthalenecarboxylic acid or derivatives
2-naphthalenecarboxamide
N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
1-naphthol
Disaccharide
O-glycosyl compound
Glycosyl compound
Alanine or derivatives
Alpha-amino acid or derivatives
Salicylic acid or derivatives
Anisole
Aryl ketone
Alkyl aryl ether
Amino saccharide
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Oxane
Vinylogous acid
Secondary alcohol
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Amino acid
Ketone
Polyol
Acetal
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Carboxylic acid
Ether
Monocarboxylic acid or derivatives
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organic nitrogen compound
Amine
Organonitrogen compound
Organic oxide
Alcohol
Hydrocarbon derivative
Primary amine
Primary aliphatic amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

aromatic ether (CHEBI:8351 )
secondary alcohol (CHEBI:8351 )
disaccharide derivative (CHEBI:8351 )
polyphenol (CHEBI:8351 )
polyketide (CHEBI:8351 )
L-alanine derivative (CHEBI:8351 )
pradimicin (CHEBI:8351 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.65 g/L	ALOGPS
logP	0.57	ALOGPS
logP	0.073	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	2.82	ChemAxon
pKa (Strongest Basic)	9.24	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	20	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	338.04 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	198.79 m³·mol⁻¹	ChemAxon
Polarizability	83.35 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

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	478.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	328.1
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	300.7
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	479.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	387.7
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	170.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1877.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	791.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	298.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	163.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	389.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	167.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	120.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	238.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	339.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	90.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	294.1
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1147.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	756.2

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Benanomicin B_TMS_1	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(=N[C@H](C)C(=O)O)O[Si](C)(C)C)C(C)=C2	standard non polar	2025-10-23	2611.48
Gas Chromatography	Benanomicin B_TMS_2	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O[Si](C)(C)C)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	905.552
Gas Chromatography	Benanomicin B_TMS_3	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O[Si](C)(C)C)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	1535.65
Gas Chromatography	Benanomicin B_TMS_4	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O[Si](C)(C)C)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	1670.32
Gas Chromatography	Benanomicin B_TMS_5	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O[Si](C)(C)C)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	2782.96
Gas Chromatography	Benanomicin B_TMS_6	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O[Si](C)(C)C)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	1512.15
Gas Chromatography	Benanomicin B_TMS_7	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O[Si](C)(C)C)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	1608.44
Gas Chromatography	Benanomicin B_TMS_8	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O[Si](C)(C)C)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	1209.06
Gas Chromatography	Benanomicin B_TMS_9	COC1=CC(O[Si](C)(C)C)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	1913.81
Gas Chromatography	Benanomicin B_TMS_10	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O[Si](C)(C)C)C(C)=C2	standard non polar	2025-10-23	2583.19
Gas Chromatography	Benanomicin B_TMS_11	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N[Si](C)(C)C)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard non polar	2025-10-23	1598.57
Gas Chromatography	Benanomicin B_TMS_1	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(=N[C@H](C)C(=O)O)O[Si](C)(C)C)C(C)=C2	standard polar	2025-10-23	3415.37
Gas Chromatography	Benanomicin B_TMS_2	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O[Si](C)(C)C)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	2557.41
Gas Chromatography	Benanomicin B_TMS_3	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O[Si](C)(C)C)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	2636.63
Gas Chromatography	Benanomicin B_TMS_4	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O[Si](C)(C)C)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	2069.89
Gas Chromatography	Benanomicin B_TMS_5	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O[Si](C)(C)C)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	3418.91
Gas Chromatography	Benanomicin B_TMS_6	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O[Si](C)(C)C)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	-585.137
Gas Chromatography	Benanomicin B_TMS_7	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O[Si](C)(C)C)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	1432.03
Gas Chromatography	Benanomicin B_TMS_8	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O[Si](C)(C)C)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	2762.38
Gas Chromatography	Benanomicin B_TMS_9	COC1=CC(O[Si](C)(C)C)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	1144.04
Gas Chromatography	Benanomicin B_TMS_10	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O[Si](C)(C)C)C(C)=C2	standard polar	2025-10-23	1344.61
Gas Chromatography	Benanomicin B_TMS_11	COC1=CC(O)=C2C(=O)C3=C(C(=O)C2=C1)C(O)=C1C(=C3)[C@H](O)[C@@H](O[C@@H]2O[C@H](C)[C@H](N[Si](C)(C)C)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)C2=C1C(O)=C(C(O)=N[C@H](C)C(=O)O)C(C)=C2	standard polar	2025-10-23	2587.07

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	Actinobacteria	2	Human ; Human feces; Human saliva; Human urine; Human supragingival plaque; Human sputum; Human subgingival plaque	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

C00017595

Chemspider ID

4576632

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5464366

PDB ID

Not Available

ChEBI ID

8351

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 Benanomicin B (MMDBc0001397)

MOL for #<Metabolite:0x00007f9aa017b230>

3D MOL for #<Metabolite:0x00007f9aa017b230>

3D SDF for #<Metabolite:0x00007f9aa017b230>

3D-SDF for #<Metabolite:0x00007f9aa017b230>

PDB for #<Metabolite:0x00007f9aa017b230>

3D PDB for #<Metabolite:0x00007f9aa017b230>

SMILES for #<Metabolite:0x00007f9aa017b230>

INCHI for #<Metabolite:0x00007f9aa017b230>

Structure for #<Metabolite:0x00007f9aa017b230>

3D Structure for #<Metabolite:0x00007f9aa017b230>