NP-MRD: Showing NP-Card for Crocusatin B (NP0331995)

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Record Information

Version

2.0

Created at

2023-10-17 16:22:28 UTC

Updated at

2024-09-03 04:17:38 UTC

NP-MRD ID

NP0331995

Natural Product DOI

https://doi.org/10.57994/1116

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Crocusatin B

Description

Crocusatin B belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl). Crocusatin B was first documented in 2023 (PMID: 37714249). Based on a literature review very few articles have been published on Crocusatin B.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 29  0  0  0  0  0  0  0  0999 V2000
    0.4753   -1.9030   -1.1953 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3107   -0.6948   -0.3695 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3372    0.0743   -0.0970 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6732   -0.2123   -0.5826 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9001   -1.2099   -1.2844 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7533    0.6079   -0.2886 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1529    1.3027    0.7462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1377    1.9449    0.2760 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3118    3.1127    1.0102 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2493    1.0000    0.6140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0587   -0.3969    0.1331 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0015   -0.6163   -1.0389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4239   -1.3427    1.2526 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1798   -2.6507   -0.7655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4921   -2.4449   -1.3287 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8559   -1.6950   -2.2287 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2677    0.5074    0.5716 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9917    1.9827    0.6109 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0307    0.9551    1.7867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0639    2.1348   -0.8212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3265    3.8760    0.4054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3372    1.0161    1.7404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2178    1.4348    0.2422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3628   -1.6557   -1.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4528   -0.4305   -1.9959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8770    0.0459   -0.9684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5405   -1.6298    1.8525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1648   -0.8713    1.9592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9102   -2.2416    0.8035 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  6
 11 13  1  0
  3  4  1  0
  4  6  1  0
  4  5  2  0
 11  2  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  6
  9 21  1  0
 10 22  1  0
 10 23  1  0
 12 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 13 28  1  0
 13 29  1  0
  6 17  1  0
M  END


  Mrv1652304282220052D          

 13 13  0  0  1  0            999 V2000
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   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
    0.7145   -0.4125    0.0000 C   0  0  0  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
    0.3272    1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1018    1.9659    0.0000 C   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
   -0.7145   -0.4125    0.0000 C   0  0  0  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
   -1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  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
  1  6  1  0  0  0  0
  5  7  1  1  0  0  0
  3  8  1  0  0  0  0
  3  9  1  0  0  0  0
  2 10  1  0  0  0  0
  1 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331995

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O3/c1-6-8(9(12)13)4-7(11)5-10(6,2)3/h7,11H,4-5H2,1-3H3,(H,12,13)/t7-/m0/s1

> <INCHI_KEY>
HMGSPQHNDSWPPQ-ZETCQYMHSA-N

> <FORMULA>
C10H16O3

> <MOLECULAR_WEIGHT>
184.235

> <EXACT_MASS>
184.109944375

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
19.91636074888388

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5R)-5-hydroxy-2,3,3-trimethylcyclohex-1-ene-1-carboxylic acid

> <ALOGPS_LOGP>
1.32

> <JCHEM_LOGP>
1.1842531650000003

> <ALOGPS_LOGS>
-1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.17774262736139

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.788548329532808

> <JCHEM_PKA_STRONGEST_BASIC>
-2.734478800088641

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
49.696999999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5R)-5-hydroxy-2,3,3-trimethylcyclohex-1-ene-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.611   3.670   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.057   3.670   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
CONECT    1    2    6   11                                                  
CONECT    2    1    3   10                                                  
CONECT    3    2    4    8    9                                             
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5                                                            
CONECT    8    3                                                            
CONECT    9    3                                                            
CONECT   10    2                                                            
CONECT   11    1   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₆O₃

Average Mass

184.2350 Da

Monoisotopic Mass

184.10994 Da

IUPAC Name

(5R)-5-hydroxy-2,3,3-trimethylcyclohex-1-ene-1-carboxylic acid

Traditional Name

(5R)-5-hydroxy-2,3,3-trimethylcyclohex-1-ene-1-carboxylic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C10H16O3/c1-6-8(9(12)13)4-7(11)5-10(6,2)3/h7,11H,4-5H2,1-3H3,(H,12,13)/t7-/m0/s1

InChI Key

HMGSPQHNDSWPPQ-ZETCQYMHSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2023-10-17	View Spectrum

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

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600, CD₃OD, simulated)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-14	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
erecta		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Secondary alcohols

Alternative Parents

Substituents

Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Carbonyl group
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	1.32	ALOGPS
logP	1.18	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	4.79	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	49.7 m³·mol⁻¹	ChemAxon
Polarizability	19.92 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

C00032860

Chemspider ID

8165508

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9989926

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Crocusatin B (NP0331995)

MOL for NP0331995 (Crocusatin B)

3D MOL for NP0331995 (Crocusatin B)

3D SDF for NP0331995 (Crocusatin B)

3D-SDF for NP0331995 (Crocusatin B)

PDB for NP0331995 (Crocusatin B)

3D PDB for NP0331995 (Crocusatin B)

SMILES for NP0331995 (Crocusatin B)

INCHI for NP0331995 (Crocusatin B)

Structure for NP0331995 (Crocusatin B)

3D Structure for NP0331995 (Crocusatin B)