NP-MRD: Showing NP-Card for Ectoine (NP0021264)

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Record Information

Version

1.0

Created at

2021-01-06 06:31:59 UTC

Updated at

2021-08-20 00:00:00 UTC

NP-MRD ID

NP0021264

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ectoine

Provided By

NPAtlas

Description

Ectoine, also known as pyrostatin b, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. Ectoine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Ectoine is found in Ectothiorhodospira, Methylobacter marinus, Paraburkholderia phymatum, Streptomyces clavuligerus, Streptomyces katsurahamanus and Streptomyces rimosus. It was first documented in 1985 (PMID: 3838936). Based on a literature review a significant number of articles have been published on Ectoine (PMID: 22409530) (PMID: 30087103) (PMID: 34383398) (PMID: 34383397).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242120413D          

 20 20  0  0  0  0            999 V2000
    2.7944   -0.3688    0.1098 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3988    0.1483   -0.0369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2058    1.3415   -0.5099 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0901    1.8808   -0.6979 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1157    0.7692   -0.8492 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0471   -0.0625    0.3637 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0233   -1.0315    0.7154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8372   -0.9577    1.6632 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1240   -2.1671   -0.1390 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3159   -0.6802    0.3402 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5139    0.0666   -0.5922 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8062   -1.4607    0.1264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0700    0.0197    1.1553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2183    2.7185   -1.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3503    2.3262    0.3349 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8585    0.1869   -1.7675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1258    1.2687   -0.9773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9956    0.7065    1.2307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7515   -3.0311    0.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4325   -1.6731    0.5696 H   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
  3  4  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  2  0  0  0  0
  7  9  1  0  0  0  0
  6 10  1  0  0  0  0
 10  2  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  4 14  1  0  0  0  0
  4 15  1  0  0  0  0
  5 16  1  0  0  0  0
  5 17  1  0  0  0  0
  6 18  1  1  0  0  0
  9 19  1  0  0  0  0
 10 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021264

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@@]1([H])N([H])C(=NC([H])([H])C1([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C6H10N2O2/c1-4-7-3-2-5(8-4)6(9)10/h5H,2-3H2,1H3,(H,7,8)(H,9,10)/t5-/m0/s1

> <INCHI_KEY>
WQXNXVUDBPYKBA-YFKPBYRVSA-N

> <FORMULA>
C6H10N2O2

> <MOLECULAR_WEIGHT>
142.1558

> <EXACT_MASS>
142.074227574

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.253895179555728

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid

> <ALOGPS_LOGP>
-0.23

> <JCHEM_LOGP>
-2.525868016561477

> <ALOGPS_LOGS>
-1.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.746020462418522

> <JCHEM_PKA_STRONGEST_BASIC>
10.525331945460499

> <JCHEM_POLAR_SURFACE_AREA>
61.690000000000005

> <JCHEM_REFRACTIVITY>
35.0427

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ectoine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       2.794  -0.369   0.110  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.399   0.148  -0.037  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.206   1.341  -0.510  0.00  0.00           N+0
HETATM    4  C   UNK     0      -0.090   1.881  -0.698  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.116   0.769  -0.849  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.047  -0.063   0.364  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.023  -1.032   0.715  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.837  -0.958   1.663  0.00  0.00           O+0
HETATM    9  O   UNK     0      -2.124  -2.167  -0.139  0.00  0.00           O+0
HETATM   10  N   UNK     0       0.316  -0.680   0.340  0.00  0.00           N+0
HETATM   11  H   UNK     0       3.514   0.067  -0.592  0.00  0.00           H+0
HETATM   12  H   UNK     0       2.806  -1.461   0.126  0.00  0.00           H+0
HETATM   13  H   UNK     0       3.070   0.020   1.155  0.00  0.00           H+0
HETATM   14  H   UNK     0      -0.218   2.719  -1.372  0.00  0.00           H+0
HETATM   15  H   UNK     0      -0.350   2.326   0.335  0.00  0.00           H+0
HETATM   16  H   UNK     0      -0.859   0.187  -1.768  0.00  0.00           H+0
HETATM   17  H   UNK     0      -2.126   1.269  -0.977  0.00  0.00           H+0
HETATM   18  H   UNK     0      -0.996   0.707   1.231  0.00  0.00           H+0
HETATM   19  H   UNK     0      -1.752  -3.031   0.333  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.433  -1.673   0.570  0.00  0.00           H+0
CONECT    1    2   11   12   13                                             
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   14   15                                             
CONECT    5    4    6   16   17                                             
CONECT    6    5    7   10   18                                             
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   19                                                       
CONECT   10    6    2   20                                                  
CONECT   11    1                                                            
CONECT   12    1                                                            
CONECT   13    1                                                            
CONECT   14    4                                                            
CONECT   15    4                                                            
CONECT   16    5                                                            
CONECT   17    5                                                            
CONECT   18    6                                                            
CONECT   19    9                                                            
CONECT   20   10                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(+)-1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid	ChEBI
L-Ectoine	ChEBI
(4S)-2-Methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate	Kegg
(+)-1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylate	Generator
(4S)-2-Methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid	Generator
1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid	HMDB
Ectoin	HMDB
(4S)-2-Methyl-3,4,5,6-tetrahydropyrimidine-4-carboxylic acid	HMDB
(4S)-3,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid	HMDB
(S)-2-Methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid	HMDB
Pyrostatin b	HMDB
Pyrostatine b	HMDB
Ectoine	HMDB

Chemical Formula

C₆H₁₀N₂O₂

Average Mass

142.1558 Da

Monoisotopic Mass

142.07423 Da

IUPAC Name

(4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid

Traditional Name

ectoine

CAS Registry Number

Not Available

SMILES

CC1=NCC[C@H](N1)C(O)=O

InChI Identifier

InChI=1S/C6H10N2O2/c1-4-7-3-2-5(8-4)6(9)10/h5H,2-3H2,1H3,(H,7,8)(H,9,10)/t5-/m0/s1

InChI Key

WQXNXVUDBPYKBA-YFKPBYRVSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Ectothiorhodospira	NPAtlas	3838936
Methylobacter marinus	LOTUS Database	35616633
Paraburkholderia phymatum	-	KNApSAcK
Streptomyces clavuligerus	LOTUS Database	35616633
Streptomyces katsurahamanus	LOTUS Database	35616633
Streptomyces rimosus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Not Available

Substituents

Not Available

Molecular Framework

Aliphatic heteromonocyclic 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	20480 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-0.23	ALOGPS
logP	-2.5	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	2.75	ChemAxon
pKa (Strongest Basic)	10.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	61.69 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	35.04 m³·mol⁻¹	ChemAxon
Polarizability	14.25 Å³	ChemAxon
Number of Rings	1	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

NPAtlas ID

NPA024861

HMDB ID

HMDB0240650

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Ectoine

METLIN ID

Not Available

PubChem Compound

126041

PDB ID

Not Available

ChEBI ID

27592

Good Scents ID

rw1731791

References

General References

Galinski EA, Pfeiffer HP, Truper HG: 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid. A novel cyclic amino acid from halophilic phototrophic bacteria of the genus Ectothiorhodospira. Eur J Biochem. 1985 May 15;149(1):135-9. doi: 10.1111/j.1432-1033.1985.tb08903.x. [PubMed:3838936 ]
Zhang T, Creek DJ, Barrett MP, Blackburn G, Watson DG: Evaluation of coupling reversed phase, aqueous normal phase, and hydrophilic interaction liquid chromatography with Orbitrap mass spectrometry for metabolomic studies of human urine. Anal Chem. 2012 Feb 21;84(4):1994-2001. doi: 10.1021/ac2030738. Epub 2012 Feb 1. [PubMed:22409530 ]
Mair RD, Sirich TL, Plummer NS, Meyer TW: Characteristics of Colon-Derived Uremic Solutes. Clin J Am Soc Nephrol. 2018 Sep 7;13(9):1398-1404. doi: 10.2215/CJN.03150318. Epub 2018 Aug 7. [PubMed:30087103 ]
Mitchell PM: The cost-effectiveness of what in health and care?. 2021 Feb. [PubMed:34383398 ]
Authors unspecified: Ozanimod. 2012. [PubMed:34383397 ]

Showing NP-Card for Ectoine (NP0021264)

MOL for NP0021264 (Ectoine)

3D MOL for NP0021264 (Ectoine)

3D SDF for NP0021264 (Ectoine)

3D-SDF for NP0021264 (Ectoine)

PDB for NP0021264 (Ectoine)

3D PDB for NP0021264 (Ectoine)

SMILES for NP0021264 (Ectoine)

INCHI for NP0021264 (Ectoine)

Structure for NP0021264 (Ectoine)

3D Structure for NP0021264 (Ectoine)