NP-MRD: Showing NP-Card for Nocamycin I (NP0140566)

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Record Information

Version

2.0

Created at

2022-06-29 21:40:40 UTC

Updated at

2022-06-29 21:40:40 UTC

NP-MRD ID

NP0140566

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nocamycin I

Description

Nocamycin I, also known as bu 2313B, belongs to the class of organic compounds known as furopyrans. These are organic polycyclic compounds containing a furan ring fused to a pyran ring. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom. Pyran a six-membered heterocyclic, non-aromatic ring, made up of five carbon atoms and one oxygen atom and containing two double bonds. Nocamycin I is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Nocamycin I was first documented in 1982 (PMID: 6920296). Based on a literature review a small amount of articles have been published on nocamycin I (PMID: 33391238) (PMID: 33136202) (PMID: 28818448).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306292223402D          

 36 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306292223402D          

 36 39  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0140566

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)[C@H]1[C@@H](C)O[C@@]2(C)CC(=O)[C@H]3O[C@@]12O[C@H]([C@H](C)\C=C(/C)\C=C\C(\O)=C1\C(=O)CNC1=O)[C@H]3C

> <INCHI_IDENTIFIER>
InChI=1S/C26H33NO9/c1-12(7-8-16(28)19-18(30)11-27-23(19)31)9-13(2)21-14(3)22-17(29)10-25(5)26(35-21,36-22)20(15(4)34-25)24(32)33-6/h7-9,13-15,20-22,28H,10-11H2,1-6H3,(H,27,31)/b8-7+,12-9+,19-16+/t13-,14-,15-,20-,21-,22+,25+,26+/m1/s1

> <INCHI_KEY>
DTURANKMSHIDDI-GMYASLLUSA-N

> <FORMULA>
C26H33NO9

> <MOLECULAR_WEIGHT>
503.548

> <EXACT_MASS>
503.215531647

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
51.50334999664507

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1S,2S,3R,5S,8S,9R,10R)-10-[(2R,3E,5E)-7-[(3E)-2,4-dioxopyrrolidin-3-ylidene]-7-hydroxy-4-methylhepta-3,5-dien-2-yl]-3,5,9-trimethyl-7-oxo-4,11,12-trioxatricyclo[6.3.1.0^{1,5}]dodecane-2-carboxylate

> <ALOGPS_LOGP>
1.94

> <JCHEM_LOGP>
1.8477158509999998

> <ALOGPS_LOGS>
-3.75

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.71861055314529

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.312747661321416

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6931053995842178

> <JCHEM_POLAR_SURFACE_AREA>
137.45999999999998

> <JCHEM_REFRACTIVITY>
129.1188

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.92e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1S,2S,3R,5S,8S,9R,10R)-10-[(2R,3E,5E)-7-[(3E)-2,4-dioxopyrrolidin-3-ylidene]-7-hydroxy-4-methylhepta-3,5-dien-2-yl]-3,5,9-trimethyl-7-oxo-4,11,12-trioxatricyclo[6.3.1.0^{1,5}]dodecane-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

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       9.107   1.857   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.586   2.095   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.612   0.797   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.625  -0.486   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.241  -1.897   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.042  -0.339   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.469   1.170   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.404   2.510   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.522   1.665   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.326   3.677   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.886   3.111   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.977   1.566   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.588   3.941   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.671   5.178   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.143   5.630   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.543   6.227   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.887   7.728   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.470   3.767   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       7.061   3.607   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.016   4.815   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.540   4.593   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.447   6.246   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.401   7.455   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.925   7.232   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.832   8.886   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.787  10.094   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.218  11.525   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.173  12.733   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.756  14.216   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       7.312  14.751   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      10.038  15.070   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      11.246  14.116   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      10.711  12.671   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      11.566  11.390   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       6.694  11.748   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       2.437   0.026   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   12   36                                             
CONECT    8    7    9   10   18                                             
CONECT    9    8    3                                                       
CONECT   10    8   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11    7                                                       
CONECT   13   11                                                            
CONECT   14   10   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16                                                            
CONECT   18    8   19                                                       
CONECT   19   18    2   20                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   35                                                  
CONECT   28   27   29   33                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   28   34                                                  
CONECT   34   33                                                            
CONECT   35   27                                                            
CONECT   36    7                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Value	Source
(-)-Nocamycin I	ChEBI
Antibiotic bu 2313b	ChEBI
BU 2313b	ChEBI
Bu-2313b	ChEBI
Methyl (1S,2S,3R,5S,8S,9R,10R)-10-[(2R,3E,5E,7E)-7-(2,4-dioxopyrrolidin-3-ylidene)-7-hydroxy-4-methylhepta-3,5-dien-2-yl]-3,5,9-trimethyl-7-oxo-4,11,12-trioxatricyclo[6.3.1.0(1,5)]dodecane-2-carboxylate	ChEBI
Methyl (1S,2S,3R,5S,8S,9R,10R)-10-[(2R,3E,5E,7E)-7-(2,4-dioxopyrrolidin-3-ylidene)-7-hydroxy-4-methylhepta-3,5-dien-2-yl]-3,5,9-trimethyl-7-oxo-4,11,12-trioxatricyclo[6.3.1.0(1,5)]dodecane-2-carboxylic acid	Generator

Chemical Formula

C₂₆H₃₃NO₉

Average Mass

503.5480 Da

Monoisotopic Mass

503.21553 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

COC(=O)[C@H]1[C@@H](C)O[C@@]2(C)CC(=O)[C@H]3O[C@@]12O[C@H]([C@H](C)\C=C(/C)\C=C\C(\O)=C1\C(=O)CNC1=O)[C@H]3C

InChI Identifier

InChI=1S/C26H33NO9/c1-12(7-8-16(28)19-18(30)11-27-23(19)31)9-13(2)21-14(3)22-17(29)10-25(5)26(35-21,36-22)20(15(4)34-25)24(32)33-6/h7-9,13-15,20-22,28H,10-11H2,1-6H3,(H,27,31)/b8-7+,12-9+,19-16+/t13-,14-,15-,20-,21-,22+,25+,26+/m1/s1

InChI Key

DTURANKMSHIDDI-GMYASLLUSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as furopyrans. These are organic polycyclic compounds containing a furan ring fused to a pyran ring. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom. Pyran a six-membered heterocyclic, non-aromatic ring, made up of five carbon atoms and one oxygen atom and containing two double bonds.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Furopyrans

Sub Class

Not Available

Direct Parent

Furopyrans

Alternative Parents

Substituents

Furopyran
Ketal
3-pyrrolidone
2-pyrrolidone
Pyrrolidone
Pyran
Oxane
Meta-dioxane
Vinylogous acid
Methyl ester
Tetrahydrofuran
Pyrrolidine
Furan
Cyclic ketone
Secondary carboxylic acid amide
Lactam
Ketone
Carboxylic acid ester
Carboxamide group
Oxacycle
Azacycle
Monocarboxylic acid or derivatives
Ether
Enol
Dialkyl ether
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
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

76792621

KEGG Compound ID

Not Available

BioCyc ID

CPD-18224

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

54728538

PDB ID

Not Available

ChEBI ID

138066

Good Scents ID

Not Available

References

General References

Mo X, Zhang H, Du F, Yang S: Short-Chain Dehydrogenase NcmD Is Responsible for the C-10 Oxidation of Nocamycin F in Nocamycin Biosynthesis. Front Microbiol. 2020 Dec 17;11:610827. doi: 10.3389/fmicb.2020.610827. eCollection 2020. [PubMed:33391238 ]
Mo X, Yang S: Complete Genome of Nocamycin-Producing Strain Saccharothrix syringae NRRL B-16468 Reveals the Biosynthetic Potential for Secondary Metabolites. Curr Microbiol. 2021 Jan;78(1):107-113. doi: 10.1007/s00284-020-02272-0. Epub 2020 Nov 2. [PubMed:33136202 ]
Mo X, Gui C, Wang Q: Elucidation of a carboxylate O-methyltransferase NcmP in nocamycin biosynthetic pathway. Bioorg Med Chem Lett. 2017 Sep 15;27(18):4431-4435. doi: 10.1016/j.bmcl.2017.08.010. Epub 2017 Aug 7. [PubMed:28818448 ]
Bansal MB, Dhawan VK, Thadepalli H: In vitro activity of BU-2313B against anaerobic bacteria. Chemotherapy. 1982;28(3):200-3. doi: 10.1159/000238076. [PubMed:6920296 ]

Showing NP-Card for Nocamycin I (NP0140566)

MOL for NP0140566 (Nocamycin I)

3D MOL for NP0140566 (Nocamycin I)

3D SDF for NP0140566 (Nocamycin I)

3D-SDF for NP0140566 (Nocamycin I)

PDB for NP0140566 (Nocamycin I)

3D PDB for NP0140566 (Nocamycin I)

SMILES for NP0140566 (Nocamycin I)

INCHI for NP0140566 (Nocamycin I)

Structure for NP0140566 (Nocamycin I)

3D Structure for NP0140566 (Nocamycin I)