NP-MRD: Showing NP-Card for (1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid (NP0317271)

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Record Information

Version

1.0

Created at

2022-09-11 17:03:18 UTC

Updated at

2022-09-11 17:03:18 UTC

NP-MRD ID

NP0317271

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

Borrelidin 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. (1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid is found in Streptomyces albovinaceus. It was first documented in 2020 (PMID: 32253314). Based on a literature review a significant number of articles have been published on Borrelidin (PMID: 35063731) (PMID: 34804423) (PMID: 33681712) (PMID: 32250597).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112219032D          

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M  END

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M  END


  Mrv1652309112219032D          

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  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 20  1  0  0  0  0
 20 21  1  1  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  3  0  0  0  0
 28 31  1  0  0  0  0
 31 32  1  6  0  0  0
 31 33  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
  2 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0317271

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CC(C)C[C@@H](C)[C@H](O)\C(=C\C=C/C[C@@H](OC(=O)C[C@@H](O)[C@H](C)C1)[C@H]1CCC[C@@H]1C(O)=O)C#N

> <INCHI_IDENTIFIER>
InChI=1S/C28H43NO6/c1-17-12-18(2)14-20(4)27(32)21(16-29)8-5-6-11-25(22-9-7-10-23(22)28(33)34)35-26(31)15-24(30)19(3)13-17/h5-6,8,17-20,22-25,27,30,32H,7,9-15H2,1-4H3,(H,33,34)/b6-5-,21-8+/t17-,18?,19-,20-,22+,23+,24-,25-,27+/m1/s1

> <INCHI_KEY>
OJCKRNPLOZHAOU-MJQQLCDASA-N

> <FORMULA>
C28H43NO6

> <MOLECULAR_WEIGHT>
489.653

> <EXACT_MASS>
489.309038109

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
54.46397838842479

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
4.659357939333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.698482800037006

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8741594427926027

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9329410031715684

> <JCHEM_POLAR_SURFACE_AREA>
127.85000000000001

> <JCHEM_REFRACTIVITY>
135.45829999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      13.138  11.975   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.138  10.435   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.471  11.205   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.805  10.435   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.139  11.205   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      15.805   8.895   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.471   8.125   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.138   8.895   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.471   6.585   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      15.805   5.815   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.138   5.815   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.138   4.275   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      14.471   3.505   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      11.804   3.505   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      10.470   4.275   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.470   2.735   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.224   1.830   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.700   0.365   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.240   0.365   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.716   1.830   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.181   2.306   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      14.325   1.275   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      14.588   2.932   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       9.137   3.505   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.803   4.275   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.803   5.815   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.137   6.585   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.137   8.125   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.803   8.895   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       6.469   9.665   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      10.470   8.895   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      11.804   8.125   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      10.470  10.435   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       9.137  11.205   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      11.804  11.205   0.000  0.00  0.00           C+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                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   24                                                  
CONECT   16   15   17   20                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   16   21                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   15   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    2                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₃NO₆

Average Mass

489.6530 Da

Monoisotopic Mass

489.30904 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

C[C@@H]1CC(C)C[C@@H](C)[C@H](O)\C(=C\C=C/C[C@@H](OC(=O)C[C@@H](O)[C@H](C)C1)[C@H]1CCC[C@@H]1C(O)=O)C#N

InChI Identifier

InChI=1S/C28H43NO6/c1-17-12-18(2)14-20(4)27(32)21(16-29)8-5-6-11-25(22-9-7-10-23(22)28(33)34)35-26(31)15-24(30)19(3)13-17/h5-6,8,17-20,22-25,27,30,32H,7,9-15H2,1-4H3,(H,33,34)/b6-5-,21-8+/t17-,18?,19-,20-,22+,23+,24-,25-,27+/m1/s1

InChI Key

OJCKRNPLOZHAOU-MJQQLCDASA-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 albovinaceus	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
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
logP	4.66	ChemAxon
pKa (Strongest Acidic)	3.87	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	127.85 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	135.46 m³·mol⁻¹	ChemAxon
Polarizability	54.46 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

C00047195

Chemspider ID

78430624

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Borrelidin

METLIN ID

Not Available

PubChem Compound

133655849

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Li K, Chen S, Pang X, Cai J, Zhang X, Liu Y, Zhu Y, Zhou X: Natural products from mangrove sediments-derived microbes: Structural diversity, bioactivities, biosynthesis, and total synthesis. Eur J Med Chem. 2022 Feb 15;230:114117. doi: 10.1016/j.ejmech.2022.114117. Epub 2022 Jan 12. [PubMed:35063731 ]
Rakhmawatie MD, Wibawa T, Lisdiyanti P, Pratiwi WR, Damayanti E, Mustofa: Potential secondary metabolite from Indonesian Actinobacteria (InaCC A758) against Mycobacterium tuberculosis. Iran J Basic Med Sci. 2021 Aug;24(8):1058-1068. doi: 10.22038/ijbms.2021.56468.12601. [PubMed:34804423 ]
Shin J, Yang SH, Du YE, Park K, Kim D, Shin D, Kim J, Kim SH, Kim YK, Shin J, Oh DC, Kim Y: Borrelidin from Saltern-Derived Halophilic Nocardiopsis sp. Dissociates Amyloid-beta and Tau Fibrils. J Alzheimers Dis Rep. 2021 Jan 11;5(1):7-13. doi: 10.3233/ADR-200247. [PubMed:33681712 ]
Kim Y, Sundrud MS, Zhou C, Edenius M, Zocco D, Powers K, Zhang M, Mazitschek R, Rao A, Yeo CY, Noss EH, Brenner MB, Whitman M, Keller TL: Aminoacyl-tRNA synthetase inhibition activates a pathway that branches from the canonical amino acid response in mammalian cells. Proc Natl Acad Sci U S A. 2020 Apr 21;117(16):8900-8911. doi: 10.1073/pnas.1913788117. Epub 2020 Apr 6. [PubMed:32253314 ]
Curran SC, Pereira JH, Baluyot MJ, Lake J, Puetz H, Rosenburg DJ, Adams P, Keasling JD: Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster. Biochemistry. 2020 Apr 28;59(16):1630-1639. doi: 10.1021/acs.biochem.0c00126. Epub 2020 Apr 13. [PubMed:32250597 ]
LOTUS database [Link]

Showing NP-Card for (1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid (NP0317271)

MOL for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D MOL for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D SDF for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D-SDF for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

PDB for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D PDB for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

SMILES for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

INCHI for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

Structure for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)

3D Structure for NP0317271 ((1s,2s)-2-[(2r,4z,6e,8s,9r,13r,15r,16r)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxo-1-oxacyclooctadeca-4,6-dien-2-yl]cyclopentane-1-carboxylic acid)