NP-MRD: Showing NP-Card for [(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid (NP0221173)

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Record Information

Version

2.0

Created at

2022-09-05 22:40:44 UTC

Updated at

2022-09-05 22:40:44 UTC

NP-MRD ID

NP0221173

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid

Description

Ambruticin VS-4 belongs to the class of organic compounds known as delta amino acids and derivatives. Delta amino acids and derivatives are compounds containing a carboxylic acid group and an amino group at the C5 carbon atom. [(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid is found in Sorangium cellulosum. Based on a literature review very few articles have been published on Ambruticin VS-4.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062200402D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309062200402D          

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    0.3020   -3.6020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 15 16  2  0  0  0  0
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 19 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  6  0  0  0
 26 27  1  0  0  0  0
 25 28  1  0  0  0  0
 17 28  1  0  0  0  0
 28 29  1  1  0  0  0
 14 30  1  0  0  0  0
 13 30  1  0  0  0  0
 30 31  1  6  0  0  0
  5 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
  3 34  1  0  0  0  0
 34 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0221173

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H]1O[C@H](CC=C1C)C(\C)=C\[C@H](C)\C=C\[C@H]1[C@@H](C)[C@@H]1\C=C\[C@@H]1O[C@H](CC(O)=O)C[C@H](NC)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C29H45NO5/c1-7-25-18(3)9-12-26(35-25)19(4)14-17(2)8-10-22-20(5)23(22)11-13-27-29(33)24(30-6)15-21(34-27)16-28(31)32/h8-11,13-14,17,20-27,29-30,33H,7,12,15-16H2,1-6H3,(H,31,32)/b10-8+,13-11+,19-14+/t17-,20-,21+,22+,23+,24+,25-,26-,27+,29-/m1/s1

> <INCHI_KEY>
YELQROVKNIJYSH-AVZPPWFKSA-N

> <FORMULA>
C29H45NO5

> <MOLECULAR_WEIGHT>
487.681

> <EXACT_MASS>
487.329773553

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
55.77623853423239

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2S,4S,5R,6S)-6-[(E)-2-[(1S,2S,3R)-2-[(1E,3R,4E)-5-[(2R,6R)-6-ethyl-5-methyl-3,6-dihydro-2H-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid

> <JCHEM_LOGP>
1.6784189194882269

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.54723982390712

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.034235799880543

> <JCHEM_PKA_STRONGEST_BASIC>
9.874421432104754

> <JCHEM_POLAR_SURFACE_AREA>
88.02000000000001

> <JCHEM_REFRACTIVITY>
142.2655

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(2S,4S,5R,6S)-6-[(E)-2-[(1S,2S,3R)-2-[(1E,3R,4E)-5-[(2R,6R)-6-ethyl-5-methyl-3,6-dihydro-2H-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.437  -5.954   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.771  -6.724   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.105  -5.954   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.438  -6.724   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       8.772  -5.954   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.106  -6.724   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.439  -5.954   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.773  -6.724   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      14.107  -5.954   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      12.773  -8.264   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      10.106  -8.264   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.772  -9.034   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0       8.772 -10.574   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0       7.438 -11.344   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.438  -8.264   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.105  -9.034   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       1.897  -5.954   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.564  -6.724   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   34                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   32                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   30                                                  
CONECT   14   13   15   30                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   28                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   19   25                                                       
CONECT   25   24   26   28                                                  
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   25   17   29                                                  
CONECT   29   28                                                            
CONECT   30   14   13   31                                                  
CONECT   31   30                                                            
CONECT   32    5   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33    3   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₅NO₅

Average Mass

487.6810 Da

Monoisotopic Mass

487.32977 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC[C@H]1O[C@H](CC=C1C)C(\C)=C\[C@H](C)\C=C\[C@H]1[C@@H](C)[C@@H]1\C=C\[C@@H]1O[C@H](CC(O)=O)C[C@H](NC)[C@H]1O

InChI Identifier

InChI=1S/C29H45NO5/c1-7-25-18(3)9-12-26(35-25)19(4)14-17(2)8-10-22-20(5)23(22)11-13-27-29(33)24(30-6)15-21(34-27)16-28(31)32/h8-11,13-14,17,20-27,29-30,33H,7,12,15-16H2,1-6H3,(H,31,32)/b10-8+,13-11+,19-14+/t17-,20-,21+,22+,23+,24+,25-,26-,27+,29-/m1/s1

InChI Key

YELQROVKNIJYSH-AVZPPWFKSA-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
Sorangium cellulosum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as delta amino acids and derivatives. Delta amino acids and derivatives are compounds containing a carboxylic acid group and an amino group at the C5 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Delta amino acids and derivatives

Alternative Parents

Substituents

Delta amino acid or derivatives
C-glycosyl compound
Glycosyl compound
Monosaccharide
Oxane
Pyran
1,2-aminoalcohol
Amino acid
Secondary alcohol
Carboxylic acid
Dialkyl ether
Secondary aliphatic amine
Ether
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Secondary amine
Amine
Alcohol
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organic nitrogen compound
Organopnictogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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
logP	1.68	ChemAxon
pKa (Strongest Acidic)	4.03	ChemAxon
pKa (Strongest Basic)	9.87	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Rotatable Bond Count	10	ChemAxon

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

10150313

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11976966

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid (NP0221173)

MOL for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

3D MOL for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

3D SDF for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

3D-SDF for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

PDB for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

3D PDB for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

SMILES for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

INCHI for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

Structure for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)

3D Structure for NP0221173 ([(2s,4s,5r,6s)-6-[(1e)-2-[(1s,2s,3r)-2-[(1e,3r,4e)-5-[(2r,6r)-6-ethyl-5-methyl-3,6-dihydro-2h-pyran-2-yl]-3-methylhexa-1,4-dien-1-yl]-3-methylcyclopropyl]ethenyl]-5-hydroxy-4-(methylamino)oxan-2-yl]acetic acid)