NP-MRD: Showing NP-Card for Kendomycin (NP0140717)

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Record Information

Version

1.0

Created at

2022-06-29 21:48:25 UTC

Updated at

2022-06-29 21:48:25 UTC

NP-MRD ID

NP0140717

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Kendomycin

Description

Kendomycin belongs to the class of organic compounds known as benzofurans. These are organic compounds containing a benzene ring fused to a furan. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom. Kendomycin is found in Streptomyces violaceoruber. It was first documented in 2016 (PMID: 26860467). Based on a literature review a significant number of articles have been published on Kendomycin (PMID: 31765156) (PMID: 34940672) (PMID: 34833926) (PMID: 32182062).

Structure

MOL 3D MOL SDF PDB SMILES InChI


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 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
  2 26  1  0  0  0  0
 25 27  1  0  0  0  0
 23 28  1  6  0  0  0
 21 29  1  6  0  0  0
 19 30  1  6  0  0  0
 15 31  1  0  0  0  0
 12 32  1  0  0  0  0
  8 33  1  1  0  0  0
  7 34  1  6  0  0  0
  6 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0140717

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2CC[C@H](C)\C=C(C)\C[C@@H](C)C[C@H](C)[C@]3(O)OC4=C(C)C(=O)C(O)=C([C@H](O2)[C@H](C)[C@H]1O)C4=C3

> <INCHI_IDENTIFIER>
InChI=1S/C29H42O6/c1-14-8-9-22-18(5)24(30)19(6)28(34-22)23-21-13-29(33,17(4)12-16(3)11-15(2)10-14)35-27(21)20(7)25(31)26(23)32/h10,13-14,16-19,22,24,28,30,32-33H,8-9,11-12H2,1-7H3/b15-10+/t14-,16+,17-,18-,19+,22+,24-,28+,29+/m0/s1

> <INCHI_KEY>
HKLDUJXJTQJSEJ-OLXNOMCWSA-N

> <FORMULA>
C29H42O6

> <MOLECULAR_WEIGHT>
486.649

> <EXACT_MASS>
486.298139072

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0       7.386   8.836   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.077   8.024   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.126   6.485   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.483   5.757   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.532   4.218   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.889   3.490   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.937   1.951   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.629   1.139   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.271   1.867   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.223   3.406   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.963   1.055   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.698  -0.462   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.252  -0.991   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.988  -2.509   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.070  -0.004   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.335   1.513   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.605   1.783   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.557   3.322   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.200   4.050   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.384   2.725   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.151   5.589   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.794   6.317   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.745   7.856   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.054   8.668   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.411   7.940   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.720   8.752   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.460   6.401   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.612   8.584   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.687   5.477   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       0.711   4.446   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.624  -0.534   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.880  -1.449   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       7.677  -0.400   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      10.295   1.223   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      10.198   4.302   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7   35                                                  
CONECT    7    6    8   34                                                  
CONECT    8    7    9   33                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    5                                                       
CONECT   11    9   12   17                                                  
CONECT   12   11   13   32                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   31                                                  
CONECT   16   15   17   20                                                  
CONECT   17   16   11   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21   30                                             
CONECT   20   19   16                                                       
CONECT   21   19   22   29                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25    2                                                       
CONECT   27   25                                                            
CONECT   28   23                                                            
CONECT   29   21                                                            
CONECT   30   19                                                            
CONECT   31   15                                                            
CONECT   32   12                                                            
CONECT   33    8                                                            
CONECT   34    7                                                            
CONECT   35    6                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₂O₆

Average Mass

486.6490 Da

Monoisotopic Mass

486.29814 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2CC[C@H](C)\C=C(C)\C[C@@H](C)C[C@H](C)[C@]3(O)OC4=C(C)C(=O)C(O)=C([C@H](O2)[C@H](C)[C@H]1O)C4=C3

InChI Identifier

InChI=1S/C29H42O6/c1-14-8-9-22-18(5)24(30)19(6)28(34-22)23-21-13-29(33,17(4)12-16(3)11-15(2)10-14)35-27(21)20(7)25(31)26(23)32/h10,13-14,16-19,22,24,28,30,32-33H,8-9,11-12H2,1-7H3/b15-10+/t14-,16+,17-,18-,19+,22+,24-,28+,29+/m0/s1

InChI Key

HKLDUJXJTQJSEJ-OLXNOMCWSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces violaceoruber	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzofurans. These are organic compounds containing a benzene ring fused to a furan. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzofurans

Sub Class

Not Available

Direct Parent

Benzofurans

Alternative Parents

Substituents

Benzofuran
Oxane
Dihydrofuran
Vinylogous ester
Hemiacetal
Ketone
Secondary alcohol
Cyclic ketone
Ether
Enol
Dialkyl ether
Polyol
Oxacycle
Hydrocarbon derivative
Organooxygen compound
Aldehyde
Alcohol
Organic oxide
Carbonyl group
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4582118

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Kendomycin

METLIN ID

Not Available

PubChem Compound

5472093

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhang S, Xie Q, Sun C, Tian XP, Gui C, Qin X, Zhang H, Ju J: Cytotoxic Kendomycins Containing the Carbacylic Ansa Scaffold from the Marine-Derived Verrucosispora sp. SCSIO 07399. J Nat Prod. 2019 Dec 27;82(12):3366-3371. doi: 10.1021/acs.jnatprod.9b00654. Epub 2019 Nov 25. [PubMed:31765156 ]
Chen J, Zhang S, Chen Y, Tian X, Gu Y, Ju J: Identification and Heterologous Expression of the Kendomycin B Biosynthetic Gene Cluster from Verrucosispora sp. SCSIO 07399. Mar Drugs. 2021 Nov 26;19(12). pii: md19120673. doi: 10.3390/md19120673. [PubMed:34940672 ]
Paulus C, Gromyko O, Luzhetskyy A: New Kendomycin Derivative Isolated from Streptomyces sp. Cl 58-27. Molecules. 2021 Nov 12;26(22). pii: molecules26226834. doi: 10.3390/molecules26226834. [PubMed:34833926 ]
Tranter D, Filipuzzi I, Lochmann T, Knapp B, Kellosalo J, Estoppey D, Pistorius D, Meissner A, Paavilainen VO, Hoepfner D: Kendomycin Cytotoxicity against Bacterial, Fungal, and Mammalian Cells Is Due to Cation Chelation. J Nat Prod. 2020 Apr 24;83(4):965-971. doi: 10.1021/acs.jnatprod.9b00826. Epub 2020 Mar 17. [PubMed:32182062 ]
Xu S, Arimoto H: Strategies for construction of the all-carbon macrocyclic skeleton of the ansamycin antibiotic-kendomycin. J Antibiot (Tokyo). 2016 Apr;69(4):203-12. doi: 10.1038/ja.2016.5. Epub 2016 Feb 10. [PubMed:26860467 ]

Showing NP-Card for Kendomycin (NP0140717)

MOL for NP0140717 (Kendomycin)

3D MOL for NP0140717 (Kendomycin)

3D SDF for NP0140717 (Kendomycin)

3D-SDF for NP0140717 (Kendomycin)

PDB for NP0140717 (Kendomycin)

3D PDB for NP0140717 (Kendomycin)

SMILES for NP0140717 (Kendomycin)

INCHI for NP0140717 (Kendomycin)

Structure for NP0140717 (Kendomycin)

3D Structure for NP0140717 (Kendomycin)