NP-MRD: Showing NP-Card for [(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid (NP0300561)

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Record Information

Version

2.0

Created at

2022-09-10 13:00:57 UTC

Updated at

2022-09-10 13:00:57 UTC

NP-MRD ID

NP0300561

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid

Description

Ripostatin B 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. [(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid is found in Sorangium cellulosum. [(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid was first documented in 2012 (PMID: 22378713). Based on a literature review a small amount of articles have been published on Ripostatin B (PMID: 29542926) (PMID: 25112727) (PMID: 23967694) (PMID: 22378642).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102215002D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309102215002D          

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    2.1434   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  5 10  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 16 15  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 23 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  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 28 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
 16 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0300561

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CC[C@@H](O)C[C@H]1C[C@H](O)C\C(C)=C\C\C=C\C\C(CC(O)=O)=C/C(=O)O1)=C/CC1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H40O6/c1-22(13-15-24-10-6-4-7-11-24)14-16-26(31)20-28-21-27(32)17-23(2)9-5-3-8-12-25(18-29(33)34)19-30(35)36-28/h3-4,6-11,13,19,26-28,31-32H,5,12,14-18,20-21H2,1-2H3,(H,33,34)/b8-3+,22-13+,23-9+,25-19+/t26-,27-,28+/m1/s1

> <INCHI_KEY>
FFFWIYTVZAPFFC-TTXNTIIMSA-N

> <FORMULA>
C30H40O6

> <MOLECULAR_WEIGHT>
496.644

> <EXACT_MASS>
496.282489008

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
55.20887061861587

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(3E,6E,9E,12R,14S)-12-hydroxy-14-[(2R,5E)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid

> <JCHEM_LOGP>
4.971760175

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.837310871444444

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.0407289460561335

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7263624309294396

> <JCHEM_POLAR_SURFACE_AREA>
104.06000000000002

> <JCHEM_REFRACTIVITY>
145.16820000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(3E,6E,9E,12R,14S)-12-hydroxy-14-[(2R,5E)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0      -5.335  -6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001  -3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.668  -3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -8.002  -6.160   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -9.336  -3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.000  -6.160   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -3.850   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.668  -3.850   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       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.002  -6.160   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.668  -8.470   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.335 -10.780   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.668 -13.090   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.002 -12.320   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       6.668 -14.630   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.001  -8.470   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    2   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   36                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   33                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   28   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   16                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₀O₆

Average Mass

496.6440 Da

Monoisotopic Mass

496.28249 Da

IUPAC Name

2-[(3E,6E,9E,12R,14S)-12-hydroxy-14-[(2R,5E)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid

Traditional Name

[(3E,6E,9E,12R,14S)-12-hydroxy-14-[(2R,5E)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid

CAS Registry Number

Not Available

SMILES

C\C(CC[C@@H](O)C[C@H]1C[C@H](O)C\C(C)=C\C\C=C\C\C(CC(O)=O)=C/C(=O)O1)=C/CC1=CC=CC=C1

InChI Identifier

InChI=1S/C30H40O6/c1-22(13-15-24-10-6-4-7-11-24)14-16-26(31)20-28-21-27(32)17-23(2)9-5-3-8-12-25(18-29(33)34)19-30(35)36-28/h3-4,6-11,13,19,26-28,31-32H,5,12,14-18,20-21H2,1-2H3,(H,33,34)/b8-3+,22-13+,23-9+,25-19+/t26-,27-,28+/m1/s1

InChI Key

FFFWIYTVZAPFFC-TTXNTIIMSA-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 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
Fatty alcohol
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Fatty acyl
Benzenoid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Organic oxide
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	4.97	ChemAxon
pKa (Strongest Acidic)	4.04	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.06 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	145.17 m³·mol⁻¹	ChemAxon
Polarizability	55.21 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

C00016559

Chemspider ID

8566576

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10391134

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Glaus F, Dedic D, Tare P, Nagaraja V, Rodrigues L, Ainsa JA, Kunze J, Schneider G, Hartkoorn RC, Cole ST, Altmann KH: Total Synthesis of Ripostatin B and Structure-Activity Relationship Studies on Ripostatin Analogs. J Org Chem. 2018 Jul 6;83(13):7150-7172. doi: 10.1021/acs.joc.8b00193. Epub 2018 Mar 29. [PubMed:29542926 ]
Tang W, Liu S, Degen D, Ebright RH, Prusov EV: Synthesis and evaluation of novel analogues of ripostatins. Chemistry. 2014 Sep 15;20(38):12310-9. doi: 10.1002/chem.201403176. Epub 2014 Aug 11. [PubMed:25112727 ]
Glaus F, Altmann KH: Total synthesis of the myxobacterial macrolide ripostatin B. Chimia (Aarau). 2013;67(4):227-30. doi: 10.2533/chimia.2013.227. [PubMed:23967694 ]
Glaus F, Altmann KH: Total synthesis of the bacterial RNA polymerase inhibitor ripostatin B. Angew Chem Int Ed Engl. 2012 Apr 2;51(14):3405-9. doi: 10.1002/anie.201200871. Epub 2012 Feb 29. [PubMed:22378713 ]
Tang W, Prusov EV: Total synthesis of RNA-polymerase inhibitor ripostatin B and 15-deoxyripostatin A. Angew Chem Int Ed Engl. 2012 Apr 2;51(14):3401-4. doi: 10.1002/anie.201108749. Epub 2012 Feb 29. [PubMed:22378642 ]
LOTUS database [Link]

Showing NP-Card for [(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid (NP0300561)

MOL for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

3D MOL for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

3D SDF for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

3D-SDF for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

PDB for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

3D PDB for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

SMILES for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

INCHI for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

Structure for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)

3D Structure for NP0300561 ([(3e,6e,9e,12r,14s)-12-hydroxy-14-[(2r,5e)-2-hydroxy-5-methyl-7-phenylhept-5-en-1-yl]-10-methyl-2-oxo-1-oxacyclotetradeca-3,6,9-trien-4-yl]acetic acid)