NP-MRD: Showing NP-Card for (4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol (NP0244797)

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Record Information

Version

2.0

Created at

2022-09-07 05:40:19 UTC

Updated at

2022-09-07 05:40:19 UTC

NP-MRD ID

NP0244797

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

Description

Raocyclamide A belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. Based on a literature review very few articles have been published on Raocyclamide A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072207402D          

 39 43  0  0  1  0            999 V2000
    4.1827   -0.2715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309072207402D          

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  9 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  4  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 19 23  1  6  0  0  0
 22 24  1  0  0  0  0
 24 25  1  6  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 26 31  1  0  0  0  0
 24 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  4  0  0  0
 33 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
  5 38  1  0  0  0  0
 38 39  2  0  0  0  0
 35 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0244797

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](C)C1N=C(O)C2=COC(=N2)[C@H](C)N=C(O)[C@H]2COC(=N2)[C@@H](CC2=CC=CC=C2)N=C(O)C2=CSC1=N2

> <INCHI_IDENTIFIER>
InChI=1S/C27H30N6O5S/c1-4-14(2)21-27-32-20(13-39-27)24(36)29-17(10-16-8-6-5-7-9-16)26-31-18(12-38-26)22(34)28-15(3)25-30-19(11-37-25)23(35)33-21/h5-9,11,13-15,17-18,21H,4,10,12H2,1-3H3,(H,28,34)(H,29,36)(H,33,35)/t14-,15-,17+,18+,21?/m0/s1

> <INCHI_KEY>
PNCLWRPJCHTJRB-ZUTXQSCOSA-N

> <FORMULA>
C27H30N6O5S

> <MOLECULAR_WEIGHT>
550.63

> <EXACT_MASS>
550.199839264

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
57.35391189152297

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,8R,11S)-4-benzyl-18-[(2S)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

> <JCHEM_LOGP>
2.367778277017132

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.997885670489649

> <JCHEM_PKA_STRONGEST_ACIDIC>
-8.324705290226433

> <JCHEM_PKA_STRONGEST_BASIC>
13.904994800062088

> <JCHEM_POLAR_SURFACE_AREA>
158.28000000000003

> <JCHEM_REFRACTIVITY>
142.9218

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(4R,8R,11S)-4-benzyl-18-[(2S)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

> <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       7.808  -0.507   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.795   1.033   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.455   1.792   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.128   1.011   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.442   3.332   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       7.770   4.113   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       9.110   3.354   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       9.122   1.814   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      10.437   4.135   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.946   3.827   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      12.705   5.167   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      11.752   6.456   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      10.424   5.675   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      11.739   7.996   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.066   8.777   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      10.399   8.755   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      10.386  10.295   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      11.714  11.076   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       9.047  11.054   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.559  12.514   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       7.019  12.502   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.379  11.032   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       7.719  10.273   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       5.052  10.251   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.712  11.010   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.699  12.550   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.359  13.309   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.347  14.849   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.674  15.630   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.014  14.871   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.027  13.331   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       5.065   8.711   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       3.737   7.930   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       2.397   8.689   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       3.750   6.390   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.729   5.237   0.000  0.00  0.00           C+0
HETATM   37  S   UNK     0       3.510   3.910   0.000  0.00  0.00           S+0
HETATM   38  C   UNK     0       5.102   4.091   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0       5.090   5.631   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   38                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12    9                                                       
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   23                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22   19                                                       
CONECT   24   22   25   32                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   31                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   26                                                       
CONECT   32   24   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   39                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37    5   39                                                  
CONECT   39   38   35                                                       
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₀N₆O₅S

Average Mass

550.6300 Da

Monoisotopic Mass

550.19984 Da

IUPAC Name

(4R,8R,11S)-4-benzyl-18-[(2S)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

Traditional Name

(4R,8R,11S)-4-benzyl-18-[(2S)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol

CAS Registry Number

Not Available

SMILES

CC[C@H](C)C1N=C(O)C2=COC(=N2)[C@H](C)N=C(O)[C@H]2COC(=N2)[C@@H](CC2=CC=CC=C2)N=C(O)C2=CSC1=N2

InChI Identifier

InChI=1S/C27H30N6O5S/c1-4-14(2)21-27-32-20(13-39-27)24(36)29-17(10-16-8-6-5-7-9-16)26-31-18(12-38-26)22(34)28-15(3)25-30-19(11-37-25)23(35)33-21/h5-9,11,13-15,17-18,21H,4,10,12H2,1-3H3,(H,28,34)(H,29,36)(H,33,35)/t14-,15-,17+,18+,21?/m0/s1

InChI Key

PNCLWRPJCHTJRB-ZUTXQSCOSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Cyclic peptides

Alternative Parents

Substituents

Cyclic alpha peptide
Macrolactam
Alpha-amino acid or derivatives
2-heteroaryl carboxamide
Thiazolecarboxylic acid or derivatives
Monocyclic benzene moiety
Benzenoid
Azole
Heteroaromatic compound
Oxazole
Oxazoline
Thiazole
Carboxamide group
Imido ester
Lactam
Secondary carboxylic acid amide
Azacycle
Oxacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Organic nitrogen compound
Carbonyl group
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	2.37	ChemAxon
pKa (Strongest Acidic)	-8.3	ChemAxon
pKa (Strongest Basic)	13.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	158.28 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	142.92 m³·mol⁻¹	ChemAxon
Polarizability	57.35 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

C00031128

Chemspider ID

78437772

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139586607

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol (NP0244797)

MOL for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D MOL for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D SDF for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D-SDF for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

PDB for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D PDB for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

SMILES for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

INCHI for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

Structure for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)

3D Structure for NP0244797 ((4r,8r,11s)-4-benzyl-18-[(2s)-butan-2-yl]-11-methyl-6,13-dioxa-20-thia-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1⁵,⁸.1¹²,¹⁵]tetracosa-1(21),2,5(24),9,12(23),14,16,19(22)-octaene-2,9,16-triol)