NP-MRD: Showing NP-Card for (1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (NP0312673)

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Record Information

Version

2.0

Created at

2022-09-11 09:39:36 UTC

Updated at

2022-09-11 09:39:36 UTC

NP-MRD ID

NP0312673

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid

Description

Imbricatine belongs to the class of organic compounds known as benzylisoquinolines. These are organic compounds containing an isoquinoline to which a benzyl group is attached. (1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid is found in Dermasterias imbricata. Based on a literature review very few articles have been published on Imbricatine.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112211392D          

 36 39  0  0  1  0            999 V2000
    1.9432    2.9832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6077    2.2295    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0202    1.5150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4681    0.9019    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -1.2101    2.9071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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  7 14  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309112211392D          

 36 39  0  0  1  0            999 V2000
    1.9432    2.9832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0312673

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=NC(SC2=C(O)C=C(O)C3=C2C[C@@H](N[C@@H]3CC2=CC=C(O)C=C2)C(O)=O)=C1C[C@H](N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H26N4O7S/c1-28-10-26-22(17(28)8-14(25)23(32)33)36-21-13-7-16(24(34)35)27-15(20(13)18(30)9-19(21)31)6-11-2-4-12(29)5-3-11/h2-5,9-10,14-16,27,29-31H,6-8,25H2,1H3,(H,32,33)(H,34,35)/t14-,15+,16+/m0/s1

> <INCHI_KEY>
BBIABWPNIDKRLX-ARFHVFGLSA-N

> <FORMULA>
C24H26N4O7S

> <MOLECULAR_WEIGHT>
514.55

> <EXACT_MASS>
514.152220367

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
52.06220779439275

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3R)-5-({5-[(2S)-2-amino-2-carboxyethyl]-1-methyl-1H-imidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid

> <JCHEM_LOGP>
-2.647510326757509

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
1.4438138319339755

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.773441538070812

> <JCHEM_PKA_STRONGEST_BASIC>
9.929628773113897

> <JCHEM_POLAR_SURFACE_AREA>
191.16

> <JCHEM_REFRACTIVITY>
133.3213

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3R)-5-({5-[(2S)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       3.627   5.569   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.001   4.162   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       3.771   2.828   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.741   1.684   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       0.000   1.540   0.000  0.00  0.00           S+0
HETATM    7  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0       4.001  -2.310   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.495   3.842   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.350   4.872   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.114   4.396   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      -1.435   2.890   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0      -2.259   5.427   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.939   6.933   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -3.723   4.951   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   30                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   30                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   14                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   21                                                  
CONECT   14   13    7   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   16   21                                                       
CONECT   21   20   13   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   29                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   23                                                       
CONECT   30    5    2   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₆N₄O₇S

Average Mass

514.5500 Da

Monoisotopic Mass

514.15222 Da

IUPAC Name

(1R,3R)-5-({5-[(2S)-2-amino-2-carboxyethyl]-1-methyl-1H-imidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid

Traditional Name

(1R,3R)-5-({5-[(2S)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid

CAS Registry Number

Not Available

SMILES

CN1C=NC(SC2=C(O)C=C(O)C3=C2C[C@@H](N[C@@H]3CC2=CC=C(O)C=C2)C(O)=O)=C1C[C@H](N)C(O)=O

InChI Identifier

InChI=1S/C24H26N4O7S/c1-28-10-26-22(17(28)8-14(25)23(32)33)36-21-13-7-16(24(34)35)27-15(20(13)18(30)9-19(21)31)6-11-2-4-12(29)5-3-11/h2-5,9-10,14-16,27,29-31H,6-8,25H2,1H3,(H,32,33)(H,34,35)/t14-,15+,16+/m0/s1

InChI Key

BBIABWPNIDKRLX-ARFHVFGLSA-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
Dermasterias imbricata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzylisoquinolines. These are organic compounds containing an isoquinoline to which a benzyl group is attached.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isoquinolines and derivatives

Sub Class

Benzylisoquinolines

Direct Parent

Benzylisoquinolines

Alternative Parents

Substituents

Benzylisoquinoline
Histidine or derivatives
Diarylthioether
Alpha-amino acid
Tetrahydroisoquinoline
Alpha-amino acid or derivatives
D-alpha-amino acid
L-alpha-amino acid
Imidazolyl carboxylic acid derivative
Thiophenol ether
Aryl thioether
Aralkylamine
Phenol
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Dicarboxylic acid or derivatives
N-substituted imidazole
Monocyclic benzene moiety
Heteroaromatic compound
Imidazole
Azole
Amino acid or derivatives
Amino acid
Azacycle
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Sulfenyl compound
Thioether
Secondary amine
Organopnictogen compound
Amine
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Primary aliphatic amine
Primary amine
Organonitrogen compound
Organooxygen compound
Organosulfur 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	-2.6	ChemAxon
pKa (Strongest Acidic)	0.77	ChemAxon
pKa (Strongest Basic)	9.93	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	191.16 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	133.32 m³·mol⁻¹	ChemAxon
Polarizability	52.06 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	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

160389

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

184468

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (NP0312673)

MOL for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

3D MOL for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

3D SDF for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

3D-SDF for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

PDB for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

3D PDB for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

SMILES for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

INCHI for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

Structure for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)

3D Structure for NP0312673 ((1r,3r)-5-({5-[(2s)-2-amino-2-carboxyethyl]-1-methylimidazol-4-yl}sulfanyl)-6,8-dihydroxy-1-[(4-hydroxyphenyl)methyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid)