NP-MRD: Showing NP-Card for methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate (NP0197262)

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Record Information

Version

2.0

Created at

2022-09-04 15:29:26 UTC

Updated at

2022-09-04 15:29:26 UTC

NP-MRD ID

NP0197262

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate

Description

Pericosine A belongs to the class of organic compounds known as shikimic acids and derivatves. These are cyclitols containing a cyclohexanecarboxylic acid substituted with three hydroxyl groups at positions 3, 4, and 5. methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate is found in Periconia byssoides. methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate was first documented in 2009 (PMID: 19514797). Based on a literature review a small amount of articles have been published on Pericosine A (PMID: 26928999) (PMID: 35877731) (PMID: 35775430) (PMID: 31273979).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042217292D          

 14 14  0  0  1  0            999 V2000
    0.0000    3.3000    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
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0197262

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=C[C@H](O)[C@H](O)[C@H](O)[C@H]1Cl

> <INCHI_IDENTIFIER>
InChI=1S/C8H11ClO5/c1-14-8(13)3-2-4(10)6(11)7(12)5(3)9/h2,4-7,10-12H,1H3/t4-,5-,6-,7+/m0/s1

> <INCHI_KEY>
AEDMWQPFIPNFCS-ZTYPAOSTSA-N

> <FORMULA>
C8H11ClO5

> <MOLECULAR_WEIGHT>
222.62

> <EXACT_MASS>
222.0295012

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
20.061012781897237

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (3S,4S,5S,6S)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate

> <JCHEM_LOGP>
-0.8252509786666662

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.806434158022302

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.705217951098724

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3822410399878873

> <JCHEM_POLAR_SURFACE_AREA>
86.99

> <JCHEM_REFRACTIVITY>
47.987899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (3S,4S,5S,6S)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14 Cl   UNK     0      -1.334   2.310   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    5   14                                                  
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

View in JSmol

Synonyms

Value	Source
Methyl (3S,4S,5S,6S)-6-chloro-3,4,5-trihydroxy-1-cyclohexene-1-carboxylate	MeSH

Chemical Formula

C₈H₁₁ClO₅

Average Mass

222.6200 Da

Monoisotopic Mass

222.02950 Da

IUPAC Name

methyl (3S,4S,5S,6S)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate

Traditional Name

methyl (3S,4S,5S,6S)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=C[C@H](O)[C@H](O)[C@H](O)[C@H]1Cl

InChI Identifier

InChI=1S/C8H11ClO5/c1-14-8(13)3-2-4(10)6(11)7(12)5(3)9/h2,4-7,10-12H,1H3/t4-,5-,6-,7+/m0/s1

InChI Key

AEDMWQPFIPNFCS-ZTYPAOSTSA-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
Periconia byssoides	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as shikimic acids and derivatves. These are cyclitols containing a cyclohexanecarboxylic acid substituted with three hydroxyl groups at positions 3, 4, and 5.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Shikimic acids and derivatves

Alternative Parents

Substituents

Shikimic acid or derivatives
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Carboxylic acid ester
Chlorohydrin
Secondary alcohol
Halohydrin
Carboxylic acid derivative
Polyol
Monocarboxylic acid or derivatives
Alkyl chloride
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alkyl halide
Organohalogen compound
Organochloride
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic 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	-0.83	ChemAxon
pKa (Strongest Acidic)	12.71	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	47.99 m³·mol⁻¹	ChemAxon
Polarizability	20.06 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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

21376322

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16752786

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Du L, You J, Nicholas KM, Cichewicz RH: Chemoreactive Natural Products that Afford Resistance Against Disparate Antibiotics and Toxins. Angew Chem Int Ed Engl. 2016 Mar 18;55(13):4220-5. doi: 10.1002/anie.201511348. Epub 2016 Mar 1. [PubMed:26928999 ]
Usami Y, Mizobuchi Y, Ijuin M, Yamada T, Morita M, Mizuki K, Yoneyama H, Harusawa S: Synthesis of 6-Halo-Substituted Pericosine A and an Evaluation of Their Antitumor and Antiglycosidase Activities. Mar Drugs. 2022 Jun 30;20(7):438. doi: 10.3390/md20070438. [PubMed:35877731 ]
Usami Y, Nakamura K, Mizobuchi Y, Mizuki K, Harusawa S, Yoneyama H, Yamada T: Enantiomeric composition of natural pericosine A derived from Periconia byssoides and alpha-glycosidase inhibitory activity of (-)-enantiomer. Chirality. 2022 Oct;34(10):1320-1327. doi: 10.1002/chir.23491. Epub 2022 Jul 1. [PubMed:35775430 ]
Du L, Munteanu C, King JB, Frantz DE, Cichewicz RH: An Electrophilic Natural Product Provides a Safe and Robust Odor Neutralization Approach To Counteract Malodorous Organosulfur Metabolites Encountered in Skunk Spray. J Nat Prod. 2019 Jul 26;82(7):1989-1999. doi: 10.1021/acs.jnatprod.9b00415. Epub 2019 Jul 5. [PubMed:31273979 ]
Usami Y, Ohsugi M, Mizuki K, Ichikawa H, Arimoto M: Facile and efficient synthesis of naturally occurring carbasugars (+)-pericosines A and C. Org Lett. 2009 Jun 18;11(12):2699-701. doi: 10.1021/ol9008188. [PubMed:19514797 ]
LOTUS database [Link]

Showing NP-Card for methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate (NP0197262)

MOL for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

3D MOL for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

3D SDF for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

3D-SDF for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

PDB for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

3D PDB for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

SMILES for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

INCHI for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

Structure for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)

3D Structure for NP0197262 (methyl (3s,4s,5s,6s)-6-chloro-3,4,5-trihydroxycyclohex-1-ene-1-carboxylate)