NP-MRD: Showing NP-Card for (1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid (NP0172001)

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Record Information

Version

2.0

Created at

2022-09-03 08:45:27 UTC

Updated at

2022-09-03 08:45:28 UTC

NP-MRD ID

NP0172001

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid

Description

Borrelidin E belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members. (1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid is found in Streptomyces olivaceus. (1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid was first documented in 2014 (PMID: 25128830). Based on a literature review very few articles have been published on Borrelidin E.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032210452D          

 36 37  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309032210452D          

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    5.9104   -1.8980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 O   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
    1.4289   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  3  0  0  0  0
 15 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 23 27  1  0  0  0  0
 27 28  1  6  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 22 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
  2 35  1  0  0  0  0
 35 36  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0172001

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C[C@@H](C)[C@H](O)[C@@H](C)C[C@H](C)[C@@H](O)\C(=C/C=C/C[C@H](OC(=O)C[C@@H]1O)[C@@H]1CCC[C@H]1C(O)=O)C#N

> <INCHI_IDENTIFIER>
InChI=1S/C28H43NO7/c1-16-12-17(2)26(32)18(3)13-19(4)27(33)20(15-29)8-5-6-11-24(36-25(31)14-23(16)30)21-9-7-10-22(21)28(34)35/h5-6,8,16-19,21-24,26-27,30,32-33H,7,9-14H2,1-4H3,(H,34,35)/b6-5+,20-8-/t16-,17+,18-,19-,21+,22+,23-,24-,26-,27+/m0/s1

> <INCHI_KEY>
JYDQFLOVUQYSLP-KPZLOJHTSA-N

> <FORMULA>
C28H43NO7

> <MOLECULAR_WEIGHT>
505.652

> <EXACT_MASS>
505.303952729

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
54.54773875335386

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R)-2-[(2S,4E,6Z,8R,9S,11S,12S,13R,15S,16S)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid

> <ALOGPS_LOGP>
2.88

> <JCHEM_LOGP>
3.4285468723333317

> <ALOGPS_LOGS>
-4.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.698352887443907

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8741696500250344

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7545939779854466

> <JCHEM_POLAR_SURFACE_AREA>
148.07999999999998

> <JCHEM_REFRACTIVITY>
136.97380000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.92e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R)-2-[(2S,4E,6Z,8R,9S,11S,12S,13R,15S,16S)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -0.770   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  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       6.668   5.390   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.756  -5.525   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.232  -6.990   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.772  -6.990   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.248  -5.525   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.713  -5.049   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      11.857  -6.080   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      11.033  -3.543   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   35                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   31                                                  
CONECT   23   22   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   23   28                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   22   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34    2   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₃NO₇

Average Mass

505.6520 Da

Monoisotopic Mass

505.30395 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@H]1C[C@@H](C)[C@H](O)[C@@H](C)C[C@H](C)[C@@H](O)\C(=C/C=C/C[C@H](OC(=O)C[C@@H]1O)[C@@H]1CCC[C@H]1C(O)=O)C#N

InChI Identifier

InChI=1S/C28H43NO7/c1-16-12-17(2)26(32)18(3)13-19(4)27(33)20(15-29)8-5-6-11-24(36-25(31)14-23(16)30)21-9-7-10-22(21)28(34)35/h5-6,8,16-19,21-24,26-27,30,32-33H,7,9-14H2,1-4H3,(H,34,35)/b6-5+,20-8-/t16-,17+,18-,19-,21+,22+,23-,24-,26-,27+/m0/s1

InChI Key

JYDQFLOVUQYSLP-KPZLOJHTSA-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 olivaceus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolides and analogues

Sub Class

Not Available

Direct Parent

Macrolides and analogues

Alternative Parents

Substituents

Macrolide
Dicarboxylic acid or derivatives
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Nitrile
Carbonitrile
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
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

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

78441739

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139590483

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Li M, Zhang J, Liu C, Fang B, Wang X, Xiang W: Identification of borrelidin binding site on threonyl-tRNA synthetase. Biochem Biophys Res Commun. 2014 Sep 5;451(4):485-90. doi: 10.1016/j.bbrc.2014.07.100. Epub 2014 Aug 13. [PubMed:25128830 ]
LOTUS database [Link]

Showing NP-Card for (1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid (NP0172001)

MOL for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D MOL for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D SDF for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D-SDF for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

PDB for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D PDB for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

SMILES for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

INCHI for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

Structure for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D Structure for NP0172001 ((1r,2r)-2-[(2s,4e,6z,8r,9s,11s,12s,13r,15s,16s)-7-cyano-8,12,16-trihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)