NP-MRD: Showing NP-Card for (2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid (NP0256225)

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Record Information

Version

1.0

Created at

2022-09-07 20:58:25 UTC

Updated at

2022-09-07 20:58:26 UTC

NP-MRD ID

NP0256225

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid

Description

Ciliatamide A belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Ciliatamide A is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. It was first documented in 2008 (PMID: 18257536). Based on a literature review a small amount of articles have been published on ciliatamide A (PMID: 18788742) (PMID: 33367306) (PMID: 29016113) (PMID: 23465061).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072222582D          

 32 33  0  0  1  0            999 V2000
    1.7689   -8.4371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5485   -8.1670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1721   -8.7071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9517   -8.4371    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


  Mrv1652309072222582D          

 32 33  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0256225

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN([C@H](CC1=CC=CC=C1)C(O)=N[C@@H]1CCCCN=C1O)C(=O)CCCCCCCC=C

> <INCHI_IDENTIFIER>
InChI=1S/C26H39N3O3/c1-3-4-5-6-7-8-12-18-24(30)29(2)23(20-21-15-10-9-11-16-21)26(32)28-22-17-13-14-19-27-25(22)31/h3,9-11,15-16,22-23H,1,4-8,12-14,17-20H2,2H3,(H,27,31)(H,28,32)/t22-,23-/m1/s1

> <INCHI_KEY>
UNVIKJZRLTXMOH-DHIUTWEWSA-N

> <FORMULA>
C26H39N3O3

> <MOLECULAR_WEIGHT>
441.616

> <EXACT_MASS>
441.299142128

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
51.181960062433724

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-N-[(6R)-7-hydroxy-3,4,5,6-tetrahydro-2H-azepin-6-yl]-2-(N-methyldec-9-enamido)-3-phenylpropanimidic acid

> <JCHEM_LOGP>
2.9739497534609702

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.844859985542494

> <JCHEM_PKA_STRONGEST_ACIDIC>
-4.3133465873528865

> <JCHEM_PKA_STRONGEST_BASIC>
12.208284637763123

> <JCHEM_POLAR_SURFACE_AREA>
85.49000000000001

> <JCHEM_REFRACTIVITY>
128.7879

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-N-[(3R)-2-hydroxy-4,5,6,7-tetrahydro-3H-azepin-3-yl]-2-(N-methyldec-9-enamido)-3-phenylpropanimidic acid

> <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       3.302 -15.749   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.757 -15.245   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.921 -16.253   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.376 -15.749   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.541 -16.757   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.996 -16.253   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.160 -17.261   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.615 -16.757   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.779 -17.766   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      15.234 -17.261   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      15.525 -15.749   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0      16.399 -18.270   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      16.107 -19.782   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      17.854 -17.766   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      18.145 -16.253   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      19.600 -15.749   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      19.891 -14.237   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      21.346 -13.733   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      22.510 -14.741   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      22.219 -16.253   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      20.764 -16.757   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.018 -18.774   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      18.727 -20.286   0.000  0.00  0.00           O+0
HETATM   24  N   UNK     0      20.473 -18.270   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      21.637 -19.278   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      23.051 -18.666   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      24.410 -19.390   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      24.691 -20.904   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      23.683 -22.068   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      22.144 -22.006   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      21.234 -20.764   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      19.720 -21.046   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
CONECT   22   14   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   31                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   25   32                                                  
CONECT   32   31                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

View in JSmol

Synonyms

Value	Source
(R,R)-Ciliatamide a	ChEBI
Ciliatamide D	MeSH

Chemical Formula

C₂₆H₃₉N₃O₃

Average Mass

441.6160 Da

Monoisotopic Mass

441.29914 Da

IUPAC Name

(2R)-N-[(6R)-7-hydroxy-3,4,5,6-tetrahydro-2H-azepin-6-yl]-2-(N-methyldec-9-enamido)-3-phenylpropanimidic acid

Traditional Name

(2R)-N-[(3R)-2-hydroxy-4,5,6,7-tetrahydro-3H-azepin-3-yl]-2-(N-methyldec-9-enamido)-3-phenylpropanimidic acid

CAS Registry Number

Not Available

SMILES

CN([C@H](CC1=CC=CC=C1)C(O)=N[C@@H]1CCCCN=C1O)C(=O)CCCCCCCC=C

InChI Identifier

InChI=1S/C26H39N3O3/c1-3-4-5-6-7-8-12-18-24(30)29(2)23(20-21-15-10-9-11-16-21)26(32)28-22-17-13-14-19-27-25(22)31/h3,9-11,15-16,22-23H,1,4-8,12-14,17-20H2,2H3,(H,27,31)(H,28,32)/t22-,23-/m1/s1

InChI Key

UNVIKJZRLTXMOH-DHIUTWEWSA-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 dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
Phenylalanine or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid or derivatives
Amphetamine or derivatives
Caprolactam
Azepane
N-acyl-amine
Monocyclic benzene moiety
Fatty amide
Benzenoid
Fatty acyl
Tertiary carboxylic acid amide
Secondary carboxylic acid amide
Lactam
Carboxamide group
Organoheterocyclic compound
Azacycle
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

lipopeptide (CHEBI:65630 )
caprolactams (CHEBI:65630 )

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	2.97	ChemAxon
pKa (Strongest Acidic)	-4.3	ChemAxon
pKa (Strongest Basic)	12.21	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	85.49 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	128.79 m³·mol⁻¹	ChemAxon
Polarizability	51.18 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

C00038762

Chemspider ID

28532947

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25112663

PDB ID

Not Available

ChEBI ID

65630

Good Scents ID

Not Available

References

General References

Lewis JA, Daniels RN, Lindsley CW: Total synthesis of Ciliatamides A-C: stereochemical revision and the natural product-guided synthesis of unnatural analogs. Org Lett. 2008 Oct 16;10(20):4545-8. doi: 10.1021/ol801842v. Epub 2008 Sep 13. [PubMed:18788742 ]
Nakao Y, Kawatsu S, Okamoto C, Okamoto M, Matsumoto Y, Matsunaga S, van Soest RW, Fusetani N: Ciliatamides A-C, bioactive lipopeptides from the deep-sea sponge Aaptos ciliata. J Nat Prod. 2008 Mar;71(3):469-72. doi: 10.1021/np8000317. Epub 2008 Feb 8. [PubMed:18257536 ]
Fischer NH, Nielsen DS, Palmer D, Meldal M, Diness F: C-Terminal lactamization of peptides. Chem Commun (Camb). 2021 Jan 28;57(7):895-898. doi: 10.1039/d0cc06018f. [PubMed:33367306 ]
Takada K, Irie R, Suo R, Matsunaga S: Resolution of the Confusion in the Assignments of Configuration for the Ciliatamides, Acylated Dipeptides from Marine Sponges. J Nat Prod. 2017 Oct 27;80(10):2845-2849. doi: 10.1021/acs.jnatprod.7b00684. Epub 2017 Oct 10. [PubMed:29016113 ]
Imae Y, Takada K, Okada S, Ise Y, Yoshimura H, Morii Y, Matsunaga S: Isolation of ciliatamide D from a marine sponge Stelletta sp. and a reinvestigation of the configuration of ciliatamide A. J Nat Prod. 2013 Apr 26;76(4):755-8. doi: 10.1021/np300878b. Epub 2013 Mar 6. [PubMed:23465061 ]
LOTUS database [Link]

Showing NP-Card for (2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid (NP0256225)

MOL for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

3D MOL for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

3D SDF for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

3D-SDF for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

PDB for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

3D PDB for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

SMILES for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

INCHI for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

Structure for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)

3D Structure for NP0256225 ((2r)-n-[(3r)-2-hydroxy-4,5,6,7-tetrahydro-3h-azepin-3-yl]-2-(n-methyldec-9-enamido)-3-phenylpropanimidic acid)