NP-MRD: Showing NP-Card for NSC 359079 (NP0061979)

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Record Information

Version

2.0

Created at

2022-04-28 06:40:21 UTC

Updated at

2022-04-28 06:40:21 UTC

NP-MRD ID

NP0061979

Secondary Accession Numbers

None

Natural Product Identification

Common Name

NSC 359079

Description

Rebeccamycin belongs to the class of organic compounds known as indolocarbazoles. These are polycyclic aromatic compounds containing an indole fused to a carbazole. Rebeccamycin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. NSC 359079 is found in Lechevalieria aerocolonigenes C-38383, Nocardia aerocolonigens C-38383-RK-2 and Streptomyces sanyensis. NSC 359079 was first documented in 2020 (PMID: 32492063). Based on a literature review a small amount of articles have been published on rebeccamycin (PMID: 35323689) (PMID: 34885910) (PMID: 34196390) (PMID: 33979675).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208402D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282208402D          

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M  END
> <DATABASE_ID>
NP0061979

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@H]1[C@H](O)[C@@H](O)[C@@H](O[C@@H]1CO)N1C2=C(C3=CC=CC(Cl)=C13)C1=C(C(=O)NC1=O)C1=C2NC2=C(Cl)C=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C27H21Cl2N3O7/c1-38-24-13(8-33)39-27(23(35)22(24)34)32-20-10(5-3-7-12(20)29)15-17-16(25(36)31-26(17)37)14-9-4-2-6-11(28)18(9)30-19(14)21(15)32/h2-7,13,22-24,27,30,33-35H,8H2,1H3,(H,31,36,37)/t13-,22-,23-,24-,27-/m1/s1

> <INCHI_KEY>
QEHOIJJIZXRMAN-QZQSLCQPSA-N

> <FORMULA>
C27H21Cl2N3O7

> <MOLECULAR_WEIGHT>
570.38

> <EXACT_MASS>
569.0756554

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
56.075640467376374

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,21-dichloro-3-[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-methoxyoxan-2-yl]-3,13,23-triazahexacyclo[14.7.0.0^{2,10}.0^{4,9}.0^{11,15}.0^{17,22}]tricosa-1(16),2(10),4,6,8,11(15),17,19,21-nonaene-12,14-dione

> <ALOGPS_LOGP>
3.32

> <JCHEM_LOGP>
2.5896325576666657

> <ALOGPS_LOGS>
-4.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.253410607387215

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.051587590353854

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9807060813245565

> <JCHEM_POLAR_SURFACE_AREA>
146.04000000000002

> <JCHEM_REFRACTIVITY>
141.0628

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.96e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,21-dichloro-3-[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-methoxyoxan-2-yl]-3,13,23-triazahexacyclo[14.7.0.0^{2,10}.0^{4,9}.0^{11,15}.0^{17,22}]tricosa-1(16),2(10),4,6,8,11(15),17,19,21-nonaene-12,14-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  N   UNK     0       7.587  -0.762   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       8.994  -0.135   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.833   1.396   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.327   1.717   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.557   0.383   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.017   0.383   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.247   1.717   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.017   3.050   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.557   3.050   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.033   4.515   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       8.497   4.991   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       5.787   5.420   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       4.541   4.515   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.076   4.991   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.741   1.396   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.580  -0.135   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       3.986  -0.762   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       1.173  -0.762   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.073   0.144   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.088   1.675   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.495   2.302   0.000  0.00  0.00           C+0
HETATM   22 Cl   UNK     0       1.012  -2.293   0.000  0.00  0.00          Cl+0
HETATM   23  C   UNK     0      10.079   2.302   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.486   1.675   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      11.647   0.144   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.401  -0.762   0.000  0.00  0.00           C+0
HETATM   27 Cl   UNK     0      10.562  -2.293   0.000  0.00  0.00          Cl+0
HETATM   28  C   UNK     0       7.267  -2.268   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.412  -3.298   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.091  -4.805   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.627  -5.281   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.482  -4.250   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.803  -2.744   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       4.018  -4.726   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       2.873  -3.696   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       6.307  -6.787   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       7.451  -7.817   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       9.236  -5.835   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       9.876  -2.822   0.000  0.00  0.00           O+0
CONECT    1    2    5   28                                                  
CONECT    2    1    3   26                                                  
CONECT    3    2    4   23                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7   17                                                  
CONECT    7    6    8   15                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8    4   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12    8   14                                                  
CONECT   14   13                                                            
CONECT   15    7   16   21                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16    6                                                       
CONECT   18   16   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   15                                                       
CONECT   22   18                                                            
CONECT   23    3   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25    2   27                                                  
CONECT   27   26                                                            
CONECT   28    1   29   33                                                  
CONECT   29   28   30   39                                                  
CONECT   30   29   31   38                                                  
CONECT   31   30   32   36                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32   28                                                       
CONECT   34   32   35                                                       
CONECT   35   34                                                            
CONECT   36   31   37                                                       
CONECT   37   36                                                            
CONECT   38   30                                                            
CONECT   39   29                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₂₁Cl₂N₃O₇

Average Mass

570.3800 Da

Monoisotopic Mass

569.07566 Da

IUPAC Name

5,21-dichloro-3-[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-methoxyoxan-2-yl]-3,13,23-triazahexacyclo[14.7.0.0^{2,10}.0^{4,9}.0^{11,15}.0^{17,22}]tricosa-1(16),2(10),4,6,8,11(15),17,19,21-nonaene-12,14-dione

Traditional Name

CAS Registry Number

Not Available

SMILES

CO[C@H]1[C@H](O)[C@@H](O)[C@@H](O[C@@H]1CO)N1C2=C(C3=CC=CC(Cl)=C13)C1=C(C(=O)NC1=O)C1=C2NC2=C(Cl)C=CC=C12

InChI Identifier

InChI=1S/C27H21Cl2N3O7/c1-38-24-13(8-33)39-27(23(35)22(24)34)32-20-10(5-3-7-12(20)29)15-17-16(25(36)31-26(17)37)14-9-4-2-6-11(28)18(9)30-19(14)21(15)32/h2-7,13,22-24,27,30,33-35H,8H2,1H3,(H,31,36,37)/t13-,22-,23-,24-,27-/m1/s1

InChI Key

QEHOIJJIZXRMAN-QZQSLCQPSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Lechevalieria aerocolonigenes C-38383	-	KNApSAcK
Nocardia aerocolonigens C-38383-RK-2	Bacteria	KNApSAcK
Streptomyces sanyensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolocarbazoles. These are polycyclic aromatic compounds containing an indole fused to a carbazole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Carbazoles

Direct Parent

Indolocarbazoles

Alternative Parents

Substituents

Indolocarbazole
Pyrrolo[2,3-a]carbazole
Pyrroloindole
Phthalimide
N-glycosyl compound
Glycosyl compound
N-alkylindole
Isoindolone
Indole
Isoindoline
Isoindole or derivatives
Monosaccharide
Benzenoid
Substituted pyrrole
Aryl chloride
Oxane
Aryl halide
Heteroaromatic compound
Carboxylic acid imide, n-unsubstituted
Pyrrole
Carboxylic acid imide
Secondary alcohol
Carboxylic acid derivative
Dialkyl ether
Ether
Oxacycle
Azacycle
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Organopnictogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organochlorine compound (CHEBI:135511 )
N-glycosyl compound (CHEBI:135511 )
organic heterohexacyclic compound (CHEBI:135511 )
indolocarbazole (CHEBI:135511 )

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
logP	3.32	ALOGPS
logP	2.59	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	8.05	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	146.04 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	141.06 m³·mol⁻¹	ChemAxon
Polarizability	56.08 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00017865

Chemspider ID

65891

KEGG Compound ID

C19701

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Rebeccamycin

METLIN ID

Not Available

PubChem Compound

73110

PDB ID

Not Available

ChEBI ID

135511

Good Scents ID

Not Available

References

General References

Desouky SE, Abu-Elghait M, Fayed EA, Selim S, Yousuf B, Igarashi Y, Abdel-Wahab BA, Mohammed Alsuhaibani A, Sonomoto K, Nakayama J: Secondary Metabolites of Actinomycetales as Potent Quorum Sensing Inhibitors Targeting Gram-Positive Pathogens: In Vitro and In Silico Study. Metabolites. 2022 Mar 15;12(3). pii: metabo12030246. doi: 10.3390/metabo12030246. [PubMed:35323689 ]
Zenkov RG, Vlasova OA, Maksimova VP, Fetisov TI, Karpechenko NY, Ektova LV, Eremina VA, Popova VG, Usalka OG, Lesovaya EA, Belitsky GA, Yakubovskaya MG, Kirsanov KI: Molecular Mechanisms of Anticancer Activity of N-Glycosides of Indolocarbazoles LCS-1208 and LCS-1269. Molecules. 2021 Dec 2;26(23). pii: molecules26237329. doi: 10.3390/molecules26237329. [PubMed:34885910 ]
Schrinner K, Schrader M, Niebusch J, Althof K, Schwarzer FA, Nowka PF, Dinius A, Kwade A, Krull R: Macroparticle-enhanced cultivation of Lentzea aerocolonigenes: Variation of mechanical stress and combination with lecithin supplementation for a significantly increased rebeccamycin production. Biotechnol Bioeng. 2021 Oct;118(10):3984-3995. doi: 10.1002/bit.27875. Epub 2021 Jul 12. [PubMed:34196390 ]
Mohan CD, Rangappa S, Nayak SC, Jadimurthy R, Wang L, Sethi G, Garg M, Rangappa KS: Bacteria as a treasure house of secondary metabolites with anticancer potential. Semin Cancer Biol. 2021 May 9. pii: S1044-579X(21)00134-6. doi: 10.1016/j.semcancer.2021.05.006. [PubMed:33979675 ]
Schrinner K, Veiter L, Schmideder S, Doppler P, Schrader M, Munch N, Althof K, Kwade A, Briesen H, Herwig C, Krull R: Morphological and physiological characterization of filamentous Lentzea aerocolonigenes: Comparison of biopellets by microscopy and flow cytometry. PLoS One. 2020 Jun 3;15(6):e0234125. doi: 10.1371/journal.pone.0234125. eCollection 2020. [PubMed:32492063 ]

Showing NP-Card for NSC 359079 (NP0061979)

MOL for NP0061979 (NSC 359079)

3D MOL for NP0061979 (NSC 359079)

3D SDF for NP0061979 (NSC 359079)

3D-SDF for NP0061979 (NSC 359079)

PDB for NP0061979 (NSC 359079)

3D PDB for NP0061979 (NSC 359079)

SMILES for NP0061979 (NSC 359079)

INCHI for NP0061979 (NSC 359079)

Structure for NP0061979 (NSC 359079)

3D Structure for NP0061979 (NSC 359079)