NP-MRD: Showing NP-Card for 9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one (NP0299058)

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Record Information

Version

2.0

Created at

2022-09-10 10:40:46 UTC

Updated at

2022-09-10 10:40:46 UTC

NP-MRD ID

NP0299058

Secondary Accession Numbers

None

Natural Product Identification

Common Name

9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one

Description

1-Alaninechlamydocin belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. 1-Alaninechlamydocin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004201500312D          

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M  END

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  Mrv1533004201500312D          

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 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 16  1  0  0  0  0
  6 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 20 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 29 34  1  0  0  0  0
 27 35  1  0  0  0  0
 35 36  1  0  0  0  0
  2 36  1  0  0  0  0
 36 37  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0299058

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1NC(=O)C(CCCCCC(=O)C2CO2)NC(=O)C2CCCN2C(=O)C(CC2=CC=CC=C2)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H36N4O6/c1-17-24(33)30-20(15-18-9-4-2-5-10-18)27(36)31-14-8-12-21(31)26(35)29-19(25(34)28-17)11-6-3-7-13-22(32)23-16-37-23/h2,4-5,9-10,17,19-21,23H,3,6-8,11-16H2,1H3,(H,28,34)(H,29,35)(H,30,33)

> <INCHI_KEY>
QMNUPNOLDLHVTB-UHFFFAOYSA-N

> <FORMULA>
C27H36N4O6

> <MOLECULAR_WEIGHT>
512.607

> <EXACT_MASS>
512.263484895

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
53.41416276919043

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
9-benzyl-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-tetradecahydropyrrolo[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

> <ALOGPS_LOGP>
1.19

> <JCHEM_LOGP>
0.9594065706666662

> <ALOGPS_LOGS>
-3.04

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.196162202245485

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.750385356809817

> <JCHEM_PKA_STRONGEST_BASIC>
-3.367541444539142

> <JCHEM_POLAR_SURFACE_AREA>
137.21

> <JCHEM_REFRACTIVITY>
133.8719

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.66e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-benzyl-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-decahydropyrrolo[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  C   UNK     0      -6.668  -4.977   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -7.438  -3.644   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -6.668  -2.310   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -5.335  -1.540   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.001   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.667  -1.540   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.771   2.104   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.541   0.770   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0      -6.668   0.770   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -7.438   2.104   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -6.668   3.437   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -8.978   2.104   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -10.009   3.248   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -11.416   2.622   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -11.255   1.090   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      -9.748   0.770   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0     -11.082   0.000   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0     -12.416   0.770   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0     -11.082  -1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -12.416  -2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -13.749  -1.540   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -15.083  -2.310   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -16.417  -1.540   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -16.417   0.000   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -15.083   0.770   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -13.749   0.000   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0      -9.748  -2.310   0.000  0.00  0.00           N+0
HETATM   36  C   UNK     0      -8.978  -3.644   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -9.748  -4.977   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   36                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   17                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14   16                                                       
CONECT   16   15   14                                                       
CONECT   17    6   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   24                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   20   25                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   35                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   29                                                       
CONECT   35   27   36                                                       
CONECT   36   35    2   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₆N₄O₆

Average Mass

512.6070 Da

Monoisotopic Mass

512.26348 Da

IUPAC Name

9-benzyl-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-tetradecahydropyrrolo[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

Traditional Name

9-benzyl-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-decahydropyrrolo[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone

CAS Registry Number

Not Available

SMILES

CC1NC(=O)C(CCCCCC(=O)C2CO2)NC(=O)C2CCCN2C(=O)C(CC2=CC=CC=C2)NC1=O

InChI Identifier

InChI=1S/C27H36N4O6/c1-17-24(33)30-20(15-18-9-4-2-5-10-18)27(36)31-14-8-12-21(31)26(35)29-19(25(34)28-17)11-6-3-7-13-22(32)23-16-37-23/h2,4-5,9-10,17,19-21,23H,3,6-8,11-16H2,1H3,(H,28,34)(H,29,35)(H,30,33)

InChI Key

QMNUPNOLDLHVTB-UHFFFAOYSA-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
Alpha-amino acid or derivatives
Monocyclic benzene moiety
Monosaccharide
Benzenoid
Cyclic carboximidic acid
Pyrrolidine
Tertiary carboxylic acid amide
Carboxamide group
Ketone
Lactam
Dialkyl ether
Oxirane
Ether
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Organic oxygen 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	1.19	ALOGPS
logP	0.96	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	10.75	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	137.21 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	133.87 m³·mol⁻¹	ChemAxon
Polarizability	53.41 Å³	ChemAxon
Number of Rings	4	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

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

126456087

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one (NP0299058)

MOL for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D MOL for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D SDF for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D-SDF for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

PDB for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D PDB for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

SMILES for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

INCHI for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

Structure for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D Structure for NP0299058 (9-benzyl-1,4,7-trihydroxy-6-methyl-3-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)