NP-MRD: Showing NP-Card for (2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid (NP0330435)

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Record Information

Version

1.0

Created at

2022-09-12 15:47:05 UTC

Updated at

2022-09-12 15:47:06 UTC

NP-MRD ID

NP0330435

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid

Description

Joramine belongs to the class of organic compounds known as asparagine and derivatives. Asparagine and derivatives are compounds containing asparagine or a derivative thereof resulting from reaction of asparagine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. (2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid is found in Trichonephila clavata. It was first documented in 1994 (PMID: 7954940). Based on a literature review very few articles have been published on Joramine (PMID: 9414584).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122217472D          

 34 34  0  0  1  0            999 V2000
   -2.1434   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -8.2500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724   -8.6625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -7.4250    0.0000 O   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


  Mrv1652309122217472D          

 34 34  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0330435

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCCNCCC(O)=NCCCCCN=C(O)[C@H](CC(O)=N)N=C(O)CC1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C23H38N6O5/c24-10-4-11-26-14-9-21(32)27-12-2-1-3-13-28-23(34)19(16-20(25)31)29-22(33)15-17-5-7-18(30)8-6-17/h5-8,19,26,30H,1-4,9-16,24H2,(H2,25,31)(H,27,32)(H,28,34)(H,29,33)/t19-/m0/s1

> <INCHI_KEY>
OLRVCVMMESGDCI-IBGZPJMESA-N

> <FORMULA>
C23H38N6O5

> <MOLECULAR_WEIGHT>
478.594

> <EXACT_MASS>
478.290368348

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
53.76533937409341

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-N-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid

> <JCHEM_LOGP>
-6.476324046364619

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
3.729152655974225

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.8891037708664822

> <JCHEM_PKA_STRONGEST_BASIC>
12.935629585941246

> <JCHEM_POLAR_SURFACE_AREA>
200.13000000000002

> <JCHEM_REFRACTIVITY>
140.8756

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-N-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  N   UNK     0      -4.001 -11.550   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -4.001 -13.090   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.667 -13.860   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -5.335 -13.860   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.335 -15.400   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -6.668 -16.170   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -8.002 -15.400   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -8.002 -13.860   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -9.336 -16.170   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -10.669 -15.400   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0     -12.003 -16.170   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -13.337 -15.400   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -13.337 -13.860   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0     -14.670 -13.090   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0     -12.003 -13.090   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001 -16.170   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.667 -15.400   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0      -4.001 -17.710   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -2.667 -18.480   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334 -17.710   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000 -18.480   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.334 -17.710   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.667 -18.480   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0       4.001 -17.710   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       5.335 -18.480   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.335 -20.020   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       6.668 -17.710   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.002 -18.480   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       9.336 -17.710   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      10.669 -18.480   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.003 -17.710   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      13.337 -18.480   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      14.670 -17.710   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   10                                                       
CONECT   17    5   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₃₈N₆O₅

Average Mass

478.5940 Da

Monoisotopic Mass

478.29037 Da

IUPAC Name

(2S)-N-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid

Traditional Name

(2S)-N-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid

CAS Registry Number

Not Available

SMILES

NCCCNCCC(O)=NCCCCCN=C(O)[C@H](CC(O)=N)N=C(O)CC1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C23H38N6O5/c24-10-4-11-26-14-9-21(32)27-12-2-1-3-13-28-23(34)19(16-20(25)31)29-22(33)15-17-5-7-18(30)8-6-17/h5-8,19,26,30H,1-4,9-16,24H2,(H2,25,31)(H,27,32)(H,28,34)(H,29,33)/t19-/m0/s1

InChI Key

OLRVCVMMESGDCI-IBGZPJMESA-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
Nephila clavata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as asparagine and derivatives. Asparagine and derivatives are compounds containing asparagine or a derivative thereof resulting from reaction of asparagine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Asparagine and derivatives

Alternative Parents

Substituents

Asparagine or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Beta amino acid or derivatives
Phenylacetamide
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Fatty amide
N-acyl-amine
Fatty acyl
Benzenoid
Carboxamide group
Primary carboxylic acid amide
Secondary carboxylic acid amide
Secondary aliphatic amine
Secondary amine
Primary amine
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Primary aliphatic amine
Amine
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	-6.5	ChemAxon
pKa (Strongest Acidic)	-0.89	ChemAxon
pKa (Strongest Basic)	12.94	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	200.13 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	140.88 m³·mol⁻¹	ChemAxon
Polarizability	53.77 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	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

Not Available

Chemspider ID

9256458

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11081310

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yoshioka M: [Diversity of joro spider toxins]. Yakugaku Zasshi. 1997 Nov;117(10-11):700-14. doi: 10.1248/yakushi1947.117.10-11_700. [PubMed:9414584 ]
Chiba T, Akizawa T, Matsukawa M, Pan-Hou H, Yoshioka M: Finding of primitive polyamine toxins in the venom of a joro spider, Nephila clavata. Chem Pharm Bull (Tokyo). 1994 Sep;42(9):1864-9. doi: 10.1248/cpb.42.1864. [PubMed:7954940 ]
LOTUS database [Link]

Showing NP-Card for (2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid (NP0330435)

MOL for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

3D MOL for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

3D SDF for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

3D-SDF for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

PDB for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

3D PDB for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

SMILES for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

INCHI for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

Structure for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)

3D Structure for NP0330435 ((2s)-n-[5-({3-[(3-aminopropyl)amino]-1-hydroxypropylidene}amino)pentyl]-2-{[1-hydroxy-2-(4-hydroxyphenyl)ethylidene]amino}butanediimidic acid)