NP-MRD: Showing NP-Card for (3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one (NP0262668)

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Record Information

Version

2.0

Created at

2022-09-08 05:35:01 UTC

Updated at

2022-09-08 05:35:01 UTC

NP-MRD ID

NP0262668

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one

Description

Pactamide B belongs to the class of organic compounds known as monoterpenoids. Monoterpenoids are compounds containing a chain of two isoprene units. (3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one is found in Streptomyces pactum. Based on a literature review very few articles have been published on Pactamide B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082207352D          

 36 40  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309082207352D          

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  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  4  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  4  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  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
 23 22  1  4  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 29 28  1  1  0  0  0
 11 29  1  0  0  0  0
 29 30  1  0  0  0  0
  8 30  1  0  0  0  0
 30 31  1  6  0  0  0
 32 31  1  6  0  0  0
  7 32  1  0  0  0  0
 32 33  1  0  0  0  0
  3 33  1  0  0  0  0
 19 34  1  1  0  0  0
 34 35  2  0  0  0  0
 16 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0262668

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC1=C(CO)[C@H]2[C@H](C[C@@H]3[C@@H]2CC[C@@H]2\C=C\C(O)=C4C(O)=N[C@@H](CCCN=C(O)\C=C/C[C@@H]32)C4=O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H38N2O5/c1-2-16-13-18-14-21-19-5-3-7-25(34)30-12-4-6-23-28(35)27(29(36)31-23)24(33)11-9-17(19)8-10-20(21)26(18)22(16)15-32/h3,7,9,11,17-21,23,26,32-33H,2,4-6,8,10,12-15H2,1H3,(H,30,34)(H,31,36)/b7-3-,11-9+,27-24?/t17-,18+,19-,20+,21+,23+,26+/m1/s1

> <INCHI_KEY>
KWCCJORRKLRCKS-ZNOMNLQXSA-N

> <FORMULA>
C29H38N2O5

> <MOLECULAR_WEIGHT>
494.632

> <EXACT_MASS>
494.278072332

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
53.404727677313076

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E,5R,8S,9S,13R,15S,16R,18Z,25S)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0^{5,16}.0^{8,15}.0^{9,13}]octacosa-1,3,10,18,20,26-hexaen-28-one

> <JCHEM_LOGP>
2.0398334945211767

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.994719462615566

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9745356747520884

> <JCHEM_PKA_STRONGEST_BASIC>
6.821187697048781

> <JCHEM_POLAR_SURFACE_AREA>
122.71000000000002

> <JCHEM_REFRACTIVITY>
142.11860000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3E,5R,8S,9S,13R,15S,16R,18Z,25S)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0^{5,16}.0^{8,15}.0^{9,13}]octacosa-1,3,10,18,20,26-hexaen-28-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.401  -9.091   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.533  -7.818   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.003  -7.933   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.998  -6.758   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.633  -5.262   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.746  -4.198   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.423  -7.342   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.919  -6.977   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.649  -5.621   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.188  -5.574   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.998  -6.884   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.537  -6.838   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.267  -5.482   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.806  -5.436   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.536  -4.080   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      12.616  -6.746   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.886  -8.102   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      10.347  -8.148   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      12.696  -9.412   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.966 -10.768   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.776 -12.078   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.046 -13.434   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      10.507 -13.481   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       9.697 -12.171   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      10.427 -10.814   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       8.158 -12.217   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.348 -10.907   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.078  -9.551   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.268  -8.241   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.729  -8.287   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.733  -9.462   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.308  -8.878   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.812  -9.243   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      14.140  -8.717   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0      14.094  -7.178   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      15.312  -6.235   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   33                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    4    8   32                                                  
CONECT    8    7    9   30                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   29                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   35                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   34                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   11   30                                                  
CONECT   30   29    8   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31    7   33                                                  
CONECT   33   32    3                                                       
CONECT   34   19   35                                                       
CONECT   35   34   16   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₈N₂O₅

Average Mass

494.6320 Da

Monoisotopic Mass

494.27807 Da

IUPAC Name

(3E,5R,8S,9S,13R,15S,16R,18Z,25S)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0^{5,16}.0^{8,15}.0^{9,13}]octacosa-1,3,10,18,20,26-hexaen-28-one

Traditional Name

(3E,5R,8S,9S,13R,15S,16R,18Z,25S)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0^{5,16}.0^{8,15}.0^{9,13}]octacosa-1,3,10,18,20,26-hexaen-28-one

CAS Registry Number

Not Available

SMILES

CCC1=C(CO)[C@H]2[C@H](C[C@@H]3[C@@H]2CC[C@@H]2\C=C\C(O)=C4C(O)=N[C@@H](CCCN=C(O)\C=C/C[C@@H]32)C4=O)C1

InChI Identifier

InChI=1S/C29H38N2O5/c1-2-16-13-18-14-21-19-5-3-7-25(34)30-12-4-6-23-28(35)27(29(36)31-23)24(33)11-9-17(19)8-10-20(21)26(18)22(16)15-32/h3,7,9,11,17-21,23,26,32-33H,2,4-6,8,10,12-15H2,1H3,(H,30,34)(H,31,36)/b7-3-,11-9+,27-24?/t17-,18+,19-,20+,21+,23+,26+/m1/s1

InChI Key

KWCCJORRKLRCKS-ZNOMNLQXSA-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 pactum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoterpenoids. Monoterpenoids are compounds containing a chain of two isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Monoterpenoids

Alternative Parents

Substituents

Monoterpenoid
Vinylogous acid
Cyclic carboximidic acid
Pyrroline
Ketone
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Enol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	2.04	ChemAxon
pKa (Strongest Acidic)	3.97	ChemAxon
pKa (Strongest Basic)	6.82	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	122.71 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	142.12 m³·mol⁻¹	ChemAxon
Polarizability	53.4 Å³	ChemAxon
Number of Rings	5	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

146684576

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one (NP0262668)

MOL for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

3D MOL for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

3D SDF for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

3D-SDF for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

PDB for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

3D PDB for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

SMILES for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

INCHI for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

Structure for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)

3D Structure for NP0262668 ((3e,5r,8s,9s,13r,15s,16r,18z,25s)-11-ethyl-2,20,27-trihydroxy-10-(hydroxymethyl)-21,26-diazapentacyclo[23.2.1.0⁵,¹⁶.0⁸,¹⁵.0⁹,¹³]octacosa-1,3,10,18,20,26-hexaen-28-one)