NP-MRD: Showing NP-Card for (3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione (NP0245686)

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Record Information

Version

2.0

Created at

2022-09-07 06:51:30 UTC

Updated at

2022-09-07 06:51:30 UTC

NP-MRD ID

NP0245686

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione

Description

Stereocalpin A belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. (3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione is found in Stereocaulon alpinum. (3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione was first documented in 2009 (PMID: 19354233). Based on a literature review a small amount of articles have been published on Stereocalpin A (PMID: 30503384) (PMID: 29470088) (PMID: 22210374).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072208512D          

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M  END

     RDKit          3D

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M  END


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 10 15  1  0  0  0  0
  8 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 22 27  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  4  0  0  0
 29 31  1  0  0  0  0
 31 32  1  6  0  0  0
 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
  4 35  1  0  0  0  0
 35 36  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0245686

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC[C@@H]1OC(=O)[C@H](CC2=CC=CC=C2)N(C)C(=O)[C@H](CC2=CC=CC=C2)N=C(O)[C@H](C)C(=O)[C@H]1C

> <INCHI_IDENTIFIER>
InChI=1S/C29H36N2O5/c1-5-12-25-19(2)26(32)20(3)27(33)30-23(17-21-13-8-6-9-14-21)28(34)31(4)24(29(35)36-25)18-22-15-10-7-11-16-22/h6-11,13-16,19-20,23-25H,5,12,17-18H2,1-4H3,(H,30,33)/t19-,20+,23-,24-,25-/m0/s1

> <INCHI_KEY>
PKKZNSZCFXCHRE-TYCVKICSSA-N

> <FORMULA>
C29H36N2O5

> <MOLECULAR_WEIGHT>
492.616

> <EXACT_MASS>
492.262422267

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
53.09325833473418

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,9S,11S,12S)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione

> <JCHEM_LOGP>
5.835277644

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.742365442980262

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.695342549697469

> <JCHEM_PKA_STRONGEST_BASIC>
1.5649857174068635

> <JCHEM_POLAR_SURFACE_AREA>
96.27

> <JCHEM_REFRACTIVITY>
137.39230000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9S,11S,12S)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667   7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  10.010   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.667   9.240   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   6.930   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.000   9.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.000   6.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.000   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -0.000  10.780   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334  11.550   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.667  10.780   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -1.334  13.090   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.667  13.860   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.667  15.400   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -4.001  16.170   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.001  17.710   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.667  18.480   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.334  17.710   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.334  16.170   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0       0.000  13.860   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0       1.334  13.090   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.239  11.844   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       2.667  13.860   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.667  15.400   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       5.335  13.860   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       4.001  11.550   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       5.335  10.780   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   35                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   16                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
CONECT   16    8   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   28                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   22                                                       
CONECT   28   20   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    4   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₆N₂O₅

Average Mass

492.6160 Da

Monoisotopic Mass

492.26242 Da

IUPAC Name

(3S,6S,9S,11S,12S)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione

Traditional Name

(3S,6S,9S,11S,12S)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione

CAS Registry Number

Not Available

SMILES

CCC[C@@H]1OC(=O)[C@H](CC2=CC=CC=C2)N(C)C(=O)[C@H](CC2=CC=CC=C2)N=C(O)[C@H](C)C(=O)[C@H]1C

InChI Identifier

InChI=1S/C29H36N2O5/c1-5-12-25-19(2)26(32)20(3)27(33)30-23(17-21-13-8-6-9-14-21)28(34)31(4)24(29(35)36-25)18-22-15-10-7-11-16-22/h6-11,13-16,19-20,23-25H,5,12,17-18H2,1-4H3,(H,30,33)/t19-,20+,23-,24-,25-/m0/s1

InChI Key

PKKZNSZCFXCHRE-TYCVKICSSA-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
Stereocaulon alpinum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Cyclic depsipeptides

Alternative Parents

Substituents

Cyclic depsipeptide
Macrolide lactam
Alpha-amino acid ester
Macrolactam
Macrolide
Alpha-amino acid or derivatives
Monocyclic benzene moiety
Benzenoid
1,3-dicarbonyl compound
Tertiary carboxylic acid amide
Carboxamide group
Carboxylic acid ester
Ketone
Lactam
Lactone
Secondary carboxylic acid amide
Cyclic ketone
Oxacycle
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Carboxylic acid derivative
Hydrocarbon derivative
Carbonyl group
Organopnictogen compound
Organic oxide
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organic nitrogen 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	5.84	ChemAxon
pKa (Strongest Acidic)	4.7	ChemAxon
pKa (Strongest Basic)	1.56	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	96.27 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	137.39 m³·mol⁻¹	ChemAxon
Polarizability	53.09 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

28284794

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24777590

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Byeon HE, Park BK, Yim JH, Lee HK, Moon EY, Rhee DK, Pyo S: Corrigendum to "Stereocalpin A inhibits the expression of adhesion molecules in activated vascular smooth muscle cells" [Int. Immunopharmacol. 12 (2012) 315-325]. Int Immunopharmacol. 2019 Jan;66:389. doi: 10.1016/j.intimp.2018.11.030. Epub 2018 Nov 28. [PubMed:30503384 ]
Kaneda M, Inuki S, Ohno H, Oishi S: Total Synthesis and Stereochemical Revision of Stereocalpin A: Mirror-Image Approach for Stereochemical Assignments of the Peptide-Polyketide Macrocycle. J Org Chem. 2018 Mar 16;83(6):3047-3060. doi: 10.1021/acs.joc.8b00118. Epub 2018 Feb 27. [PubMed:29470088 ]
Byeon HE, Park BK, Yim JH, Lee HK, Moon EY, Rhee DK, Pyo S: Stereocalpin A inhibits the expression of adhesion molecules in activated vascular smooth muscle cells. Int Immunopharmacol. 2012 Feb;12(2):315-25. doi: 10.1016/j.intimp.2011.11.020. Epub 2011 Dec 27. [PubMed:22210374 ]
Ghosh AK, Xu CX: A convergent synthesis of the proposed structure of antitumor depsipeptide stereocalpin A. Org Lett. 2009 May 7;11(9):1963-6. doi: 10.1021/ol900412u. [PubMed:19354233 ]
LOTUS database [Link]

Showing NP-Card for (3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione (NP0245686)

MOL for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

3D MOL for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

3D SDF for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

3D-SDF for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

PDB for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

3D PDB for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

SMILES for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

INCHI for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

Structure for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)

3D Structure for NP0245686 ((3s,6s,9s,11s,12s)-3,6-dibenzyl-8-hydroxy-4,9,11-trimethyl-12-propyl-1-oxa-4,7-diazacyclododec-7-ene-2,5,10-trione)