NP-MRD: Showing NP-Card for 2-C-methyl-d-erythritol (NP0030610)

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Record Information

Version

1.0

Created at

2021-06-19 21:55:17 UTC

Updated at

2021-06-29 23:58:42 UTC

NP-MRD ID

NP0030610

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-C-methyl-d-erythritol

Provided By

JEOL Database JEOL Logo

Description

2-C-methyl-D-erythritol belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group. 2-C-methyl-d-erythritol is found in Anethum graveolens , Coriandrum sativum L., Cuminum cyminum L., Liriodendron tulipifera and Primpinella anisum L.. It was first documented in 2021 (PMID: 33925614). Based on a literature review a significant number of articles have been published on 2-C-methyl-D-erythritol (PMID: 33875076) (PMID: 33747018) (PMID: 33674379) (PMID: 33530990).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192123553D          

 21 20  0  0  0  0            999 V2000
    1.6937   -2.0081   -1.1294 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5463   -2.6434   -0.3330 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7528   -2.3095    1.0570 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6197   -4.1743   -0.4564 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1866   -4.7928    0.5465 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8129   -2.0524   -0.7816 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8105   -0.6400   -0.4673 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0520   -2.6586   -0.1118 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1903   -1.8793   -0.5086 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6631   -2.3815   -0.7794 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7225   -0.9214   -0.9935 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6055   -2.2233   -2.1992 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5356   -1.3545    1.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2884   -4.5182   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6426   -4.5314   -0.2941 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0828   -4.3504    1.3788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9223   -2.1290   -1.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7451   -0.3681   -0.5922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2221   -3.6903   -0.4290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9850   -2.6027    0.9789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9656   -2.3006   -0.0950 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  9  1  0  0  0  0
  2  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4  2  1  0  0  0  0
  2  1  1  0  0  0  0
  6  8  1  0  0  0  0
  2  3  1  1  0  0  0
  6  7  1  0  0  0  0
  4 14  1  0  0  0  0
  4 15  1  0  0  0  0
  6 17  1  6  0  0  0
  8 19  1  0  0  0  0
  8 20  1  0  0  0  0
  9 21  1  0  0  0  0
  5 16  1  0  0  0  0
  1 10  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  3 13  1  0  0  0  0
  7 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0030610

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]([H])(O[H])[C@](O[H])(C([H])([H])[H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O4/c1-5(9,3-7)4(8)2-6/h4,6-9H,2-3H2,1H3/t4-,5+/m1/s1

> <INCHI_KEY>
HGVJFBSSLICXEM-UHNVWZDZSA-N

> <FORMULA>
C5H12O4

> <MOLECULAR_WEIGHT>
136.147

> <EXACT_MASS>
136.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.37744597962763

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R)-2-methylbutane-1,2,3,4-tetrol

> <ALOGPS_LOGP>
-1.84

> <JCHEM_LOGP>
-2.188772296333333

> <ALOGPS_LOGS>
0.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.098447823363575

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.8859950940716

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9777325528655147

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
31.116799999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.42e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R)-2-methylbutane-1,2,3,4-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-21         0                                  
HETATM    1  C   UNK     0       1.694  -2.008  -1.129  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.546  -2.643  -0.333  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.753  -2.309   1.057  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.620  -4.174  -0.456  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.187  -4.793   0.547  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.813  -2.052  -0.782  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.811  -0.640  -0.467  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.052  -2.659  -0.112  0.00  0.00           C+0
HETATM    9  O   UNK     0      -3.190  -1.879  -0.509  0.00  0.00           O+0
HETATM   10  H   UNK     0       2.663  -2.381  -0.779  0.00  0.00           H+0
HETATM   11  H   UNK     0       1.722  -0.921  -0.994  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.605  -2.223  -2.199  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.536  -1.355   1.112  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.288  -4.518  -1.441  0.00  0.00           H+0
HETATM   15  H   UNK     0       1.643  -4.531  -0.294  0.00  0.00           H+0
HETATM   16  H   UNK     0       0.083  -4.350   1.379  0.00  0.00           H+0
HETATM   17  H   UNK     0      -0.922  -2.129  -1.870  0.00  0.00           H+0
HETATM   18  H   UNK     0      -1.745  -0.368  -0.592  0.00  0.00           H+0
HETATM   19  H   UNK     0      -2.222  -3.690  -0.429  0.00  0.00           H+0
HETATM   20  H   UNK     0      -1.985  -2.603   0.979  0.00  0.00           H+0
HETATM   21  H   UNK     0      -3.966  -2.301  -0.095  0.00  0.00           H+0
CONECT    1    2   10   11   12                                             
CONECT    2    6    4    1    3                                             
CONECT    3    2   13                                                       
CONECT    4    5    2   14   15                                             
CONECT    5    4   16                                                       
CONECT    6    2    8    7   17                                             
CONECT    7    6   18                                                       
CONECT    8    9    6   19   20                                             
CONECT    9    8   21                                                       
CONECT   10    1                                                            
CONECT   11    1                                                            
CONECT   12    1                                                            
CONECT   13    3                                                            
CONECT   14    4                                                            
CONECT   15    4                                                            
CONECT   16    5                                                            
CONECT   17    6                                                            
CONECT   18    7                                                            
CONECT   19    8                                                            
CONECT   20    8                                                            
CONECT   21    9                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅H₁₂O₄

Average Mass

136.1470 Da

Monoisotopic Mass

136.07356 Da

IUPAC Name

(2S,3R)-2-methylbutane-1,2,3,4-tetrol

Traditional Name

(2S,3R)-2-methylbutane-1,2,3,4-tetrol

CAS Registry Number

Not Available

SMILES

[H]OC([H])([H])[C@@]([H])(O[H])[C@](O[H])(C([H])([H])[H])C([H])([H])O[H]

InChI Identifier

InChI=1S/C5H12O4/c1-5(9,3-7)4(8)2-6/h4,6-9H,2-3H2,1H3/t4-,5+/m1/s1

InChI Key

HGVJFBSSLICXEM-UHNVWZDZSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anethum graveolens	Plant	KNApSAcK
Coriandrum sativum L.	JEOL database	Kitajima, J., et al, Phytochemistry 62, 115 (2003)
Cuminum cyminum	JEOL database	Kitajima, J., et al, Phytochemistry 62, 115 (2003)
Liriodendron tulipifera	LOTUS Database	35616633
Pimpinella anisum	JEOL database	Kitajima, J., et al, Phytochemistry 62, 115 (2003)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar alcohols

Alternative Parents

Substituents

Sugar alcohol
Tertiary alcohol
Secondary alcohol
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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	-1.8	ALOGPS
logP	-2.2	ChemAxon
logS	0.74	ALOGPS
pKa (Strongest Acidic)	12.89	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	31.12 m³·mol⁻¹	ChemAxon
Polarizability	13.38 Å³	ChemAxon
Number of Rings	0	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

Not Available

Chemspider ID

9575695

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11400799

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Pollastri S, Baccelli I, Loreto F: Isoprene: An Antioxidant Itself or a Molecule with Multiple Regulatory Functions in Plants? Antioxidants (Basel). 2021 Apr 27;10(5). pii: antiox10050684. doi: 10.3390/antiox10050684. [PubMed:33925614 ]
Qian X, Zhu J, Yuan Q, Jia Q, Jin H, Han J, Sarsaiya S, Jin L, Chen J, Guo L: Illumina Sequencing Reveals Conserved and Novel MicroRNAs of Dendrobium nobile Protocorm Involved in Synthesizing Dendrobine, a Potential Nanodrug. J Biomed Nanotechnol. 2021 Mar 1;17(3):416-425. doi: 10.1166/jbn.2021.3036. [PubMed:33875076 ]
Ameztoy K, Sanchez-Lopez AM, Munoz FJ, Bahaji A, Almagro G, Baroja-Fernandez E, Gamez-Arcas S, De Diego N, Dolezal K, Novak O, Pencik A, Alpizar A, Rodriguez-Concepcion M, Pozueta-Romero J: Proteostatic Regulation of MEP and Shikimate Pathways by Redox-Activated Photosynthesis Signaling in Plants Exposed to Small Fungal Volatiles. Front Plant Sci. 2021 Mar 5;12:637976. doi: 10.3389/fpls.2021.637976. eCollection 2021. [PubMed:33747018 ]
Mitra S, Estrada-Tejedor R, Volke DC, Phillips MA, Gershenzon J, Wright LP: Negative regulation of plastidial isoprenoid pathway by herbivore-induced beta-cyclocitral in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2021 Mar 9;118(10). pii: 2008747118. doi: 10.1073/pnas.2008747118. [PubMed:33674379 ]
Zhang Y, Bian S, Liu X, Fang N, Wang C, Liu Y, Du Y, Timko MP, Zhang Z, Zhang H: Synthesis of cembratriene-ol and cembratriene-diol in yeast via the MVA pathway. Microb Cell Fact. 2021 Feb 2;20(1):29. doi: 10.1186/s12934-021-01523-4. [PubMed:33530990 ]
Kitajima, J., et al. (2003). Kitajima, J., et al, Phytochemistry 62, 115 (2003). Phytochem..

Showing NP-Card for 2-C-methyl-d-erythritol (NP0030610)

MOL for NP0030610 (2-C-methyl-d-erythritol)

3D MOL for NP0030610 (2-C-methyl-d-erythritol)

3D SDF for NP0030610 (2-C-methyl-d-erythritol)

3D-SDF for NP0030610 (2-C-methyl-d-erythritol)

PDB for NP0030610 (2-C-methyl-d-erythritol)

3D PDB for NP0030610 (2-C-methyl-d-erythritol)

SMILES for NP0030610 (2-C-methyl-d-erythritol)

INCHI for NP0030610 (2-C-methyl-d-erythritol)

Structure for NP0030610 (2-C-methyl-d-erythritol)

3D Structure for NP0030610 (2-C-methyl-d-erythritol)