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Showing NP-Card for 4-homoectoine (NP0332116)

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Record Information
Version2.0
Created at2023-11-15 00:00:28 UTC
Updated at2024-09-03 04:18:04 UTC
NP-MRD IDNP0332116
Natural Product DOIhttps://doi.org/10.57994/1273
Secondary Accession NumbersNone
Natural Product Identification
Common Name4-homoectoine
Description783339-87-7 Is also known as homoectoine. It was first documented in 2023 (PMID: 37996925). Based on a literature review a significant number of articles have been published on 783339-87-7 (PMID: 37996924) (PMID: 37996923) (PMID: 37996922) (PMID: 37996921).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0332116 (4-homoectoine)


  Mrv2104 11152300002D          

 11 11  0  0  1  0            999 V2000
    0.8566    2.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8566    1.3632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5999    1.0053    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7834    0.2009    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2691   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4441   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0703    0.2009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1133    1.0053    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5878    0.0174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1489    0.6221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8309   -0.7710    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  4  9  1  6  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
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3D MOL for NP0332116 (4-homoectoine)

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3D SDF for NP0332116 (4-homoectoine)

  Mrv2104 11152300002D          

 11 11  0  0  1  0            999 V2000
    0.8566    2.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8566    1.3632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5999    1.0053    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7834    0.2009    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2691   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4441   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0703    0.2009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1133    1.0053    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5878    0.0174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1489    0.6221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8309   -0.7710    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  4  9  1  6  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332116

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=N[C@@H](CCCN1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H12N2O2/c1-5-8-4-2-3-6(9-5)7(10)11/h6H,2-4H2,1H3,(H,8,9)(H,10,11)/t6-/m0/s1

> <INCHI_KEY>
DUXQJVAWRJYWOK-LURJTMIESA-N

> <FORMULA>
C7H12N2O2

> <MOLECULAR_WEIGHT>
156.185

> <EXACT_MASS>
156.089877634

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.854523670349714

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-2-methyl-4,5,6,7-tetrahydro-1H-1,3-diazepine-4-carboxylic acid

> <JCHEM_LOGP>
-2.0084938412595856

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.872875388216307

> <JCHEM_PKA_STRONGEST_BASIC>
10.58976685175106

> <JCHEM_POLAR_SURFACE_AREA>
61.690000000000005

> <JCHEM_REFRACTIVITY>
39.6873

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4S)-2-methyl-4,5,6,7-tetrahydro-1H-1,3-diazepine-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0332116 (4-homoectoine)
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PDB for NP0332116 (4-homoectoine)
HEADER    PROTEIN                                 15-NOV-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-NOV-23         0                                  
HETATM    1  C   UNK     0       1.599   4.085   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.599   2.545   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.986   1.876   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       3.329   0.375   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.369  -0.829   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.829  -0.829   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.131   0.375   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       0.211   1.876   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       4.830   0.032   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.878   1.161   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.284  -1.439   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    2                                                       
CONECT    9    4   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

Download
3D PDB for NP0332116 (4-homoectoine)
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SMILES for NP0332116 (4-homoectoine)
CC1=N[C@@H](CCCN1)C(O)=O
Download
INCHI for NP0332116 (4-homoectoine)
InChI=1S/C7H12N2O2/c1-5-8-4-2-3-6(9-5)7(10)11/h6H,2-4H2,1H3,(H,8,9)(H,10,11)/t6-/m0/s1
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View in JSmol
Synonyms
ValueSource
4,5,6,7-Tetrahydro-2-methyl-1H-(1,3)-diazepine-4-carboxylic acidMeSH
HomoectoineMeSH
Chemical FormulaC7H12N2O2
Average Mass156.1850 Da
Monoisotopic Mass156.08988 Da
IUPAC Name(4S)-2-methyl-4,5,6,7-tetrahydro-1H-1,3-diazepine-4-carboxylic acid
Traditional Name(4S)-2-methyl-4,5,6,7-tetrahydro-1H-1,3-diazepine-4-carboxylic acid
CAS Registry NumberNot Available
SMILES
CC1=N[C@@H](CCCN1)C(O)=O
InChI Identifier
InChI=1S/C7H12N2O2/c1-5-8-4-2-3-6(9-5)7(10)11/h6H,2-4H2,1H3,(H,8,9)(H,10,11)/t6-/m0/s1
InChI KeyDUXQJVAWRJYWOK-LURJTMIESA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D_DEPT NMR13C NMR Spectrum (1D, 126 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2024-05-04View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500.18400144, D2O, simulated)muhaiminatul.azizah@uni-jena.deFriedrich Schiller University JenaMuhaiminatu Azizah2024-05-04View Spectrum
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2ChemAxon
pKa (Strongest Acidic)2.87ChemAxon
pKa (Strongest Basic)10.59ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area61.69 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity39.69 m³·mol⁻¹ChemAxon
Polarizability15.85 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID24188077  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound45082159  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Tumminelli C, Burlo F, Pastore S, Severini GM, Berti I, Marchini S, Zanon D, De Martino E, Tommasini A: Erythropoietic protoporphyria: case reports for clinical and therapeutic hints. Ital J Pediatr. 2023 Nov 23;49(1):156. doi: 10.1186/s13052-023-01544-2. [PubMed:37996925  ] 
  2. Steinberg N, Galleguillos D, Zaidi A, Horkey M, Sipione S: Naive Huntington's disease microglia mount a normal response to inflammatory stimuli but display a partially impaired development of innate immune tolerance that can be counteracted by ganglioside GM1. J Neuroinflammation. 2023 Nov 23;20(1):276. doi: 10.1186/s12974-023-02963-y. [PubMed:37996924  ] 
  3. Rajasundaram S, Zebardast N, Mehta P, Khawaja AP, Warwick A, Duchinski K, Burgess S, Gill D, Segre AV, Wiggs J: TIE1 and TEK signalling, intraocular pressure, and primary open-angle glaucoma: a Mendelian randomization study. J Transl Med. 2023 Nov 24;21(1):847. doi: 10.1186/s12967-023-04737-9. [PubMed:37996923  ] 
  4. Takashima Y, Yamamoto K, Degawa Y, Guo Y, Nishizawa T, Ohta H, Narisawa K: Detection and isolation of a new member of Burkholderiaceae-related endofungal bacteria from Saksenaea boninensis sp. nov., a new thermotolerant fungus in Mucorales. IMA Fungus. 2023 Nov 23;14(1):24. doi: 10.1186/s43008-023-00129-2. [PubMed:37996922  ] 
  5. Gulinaizhaer A, Yang C, Zou M, Ma S, Fan X, Wu G: Detection of monkeypox virus using helicase dependent amplification and recombinase polymerase amplification combined with lateral flow test. Virol J. 2023 Nov 23;20(1):274. doi: 10.1186/s12985-023-02223-8. [PubMed:37996921  ] 
  1. Azizah M, Pohnert G: 2-Homoectoine: An Additional Member of the Ectoine Family from Phyto- and Bacterioplankton Involved in Osmoadaptation. J Nat Prod. 2024 Jan 26;87(1):50-57. doi: 10.1021/acs.jnatprod.3c00766. Epub 2023  Dec 27. [PubMed:38150306  ]