NP-MRD: Showing NP-Card for Phomalone B (NP0332113)

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Record Information

Version

2.0

Created at

2023-11-14 20:02:09 UTC

Updated at

2024-09-03 04:18:04 UTC

NP-MRD ID

NP0332113

Natural Product DOI

https://doi.org/10.57994/1270

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phomalone B

Description

Phomalone B belongs to the class of organic compounds known as heterocyclic fatty acids. These are fatty acids containing a heterocyclic attached to the acyl chain. Based on a literature review very few articles have been published on Phomalone B.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 11142320022D          

 14 14  0  0  1  0            999 V2000
    1.2822    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6351   -1.4039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2995   -2.1576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4555   -1.3177    0.0000 O   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
  2  4  1  0  0  0  0
  5  4  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  0  0  0  0
  8  9  1  0  0  0  0
  5  9  1  0  0  0  0
  8 10  1  1  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332113

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(O)C[C@@H]1CC[C@H](O1)\C=C\C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O4/c1-7(11)6-9-3-2-8(14-9)4-5-10(12)13/h4-5,7-9,11H,2-3,6H2,1H3,(H,12,13)/b5-4+/t7?,8-,9-/m0/s1

> <INCHI_KEY>
OWGHWHYMMZURLQ-RFXNVMKZSA-N

> <FORMULA>
C10H16O4

> <MOLECULAR_WEIGHT>
200.234

> <EXACT_MASS>
200.104858995

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
21.13272018312008

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E)-3-[(2S,5S)-5-(2-hydroxypropyl)oxolan-2-yl]prop-2-enoic acid

> <JCHEM_LOGP>
0.5937019926666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.579908583313218

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.4697810734205445

> <JCHEM_PKA_STRONGEST_BASIC>
-2.5451479881687105

> <JCHEM_POLAR_SURFACE_AREA>
66.75999999999999

> <JCHEM_REFRACTIVITY>
51.9487

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2E)-3-[(2S,5S)-5-(2-hydroxypropyl)oxolan-2-yl]prop-2-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-NOV-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-NOV-23         0                                  
HETATM    1  C   UNK     0       2.393   5.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.393   4.390   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.727   3.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.147  -1.375   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.052  -2.621   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.426  -4.027   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -4.584  -2.460   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8    5                                                       
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₆O₄

Average Mass

200.2340 Da

Monoisotopic Mass

200.10486 Da

IUPAC Name

(2E)-3-[(2S,5S)-5-(2-hydroxypropyl)oxolan-2-yl]prop-2-enoic acid

Traditional Name

(2E)-3-[(2S,5S)-5-(2-hydroxypropyl)oxolan-2-yl]prop-2-enoic acid

CAS Registry Number

Not Available

SMILES

CC(O)C[C@@H]1CC[C@H](O1)\C=C\C(O)=O

InChI Identifier

InChI=1S/C10H16O4/c1-7(11)6-9-3-2-8(14-9)4-5-10(12)13/h4-5,7-9,11H,2-3,6H2,1H3,(H,12,13)/b5-4+/t7?,8-,9-/m0/s1

InChI Key

OWGHWHYMMZURLQ-RFXNVMKZSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	huanghuibin2021@163.com	School of Pharmacy, Guangdong Pharmaceutical University, 280 Huandong Road, University City，Panyu District Guangzhou 510006, China;	Hui-Bin Huang	2023-11-14	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	huanghuibin2021@163.com	School of Pharmacy, Guangdong Pharmaceutical University, 280 Huandong Road, University City，Panyu District Guangzhou 510006, China;	Hui-Bin Huang	2023-11-14	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	huanghuibin2021@163.com	School of Pharmacy, Guangdong Pharmaceutical University, 280 Huandong Road, University City，Panyu District Guangzhou 510006, China;	Hui-Bin Huang	2023-11-14	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	huanghuibin2021@163.com	School of Pharmacy, Guangdong Pharmaceutical University, 280 Huandong Road, University City，Panyu District Guangzhou 510006, China;	Hui-Bin Huang	2023-11-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	huanghuibin2021@163.com	School of Pharmacy, Guangdong Pharmaceutical University, 280 Huandong Road, University City，Panyu District Guangzhou 510006, China;	Hui-Bin Huang	2023-11-14	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)	huanghuibin2021@163.com	School of Pharmacy, Guangdong Pharmaceutical University, 280 Huandong Road, University City，Panyu District Guangzhou 510006, China;	Hui-Bin Huang	2023-11-14	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as heterocyclic fatty acids. These are fatty acids containing a heterocyclic attached to the acyl chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Heterocyclic fatty acids

Alternative Parents

Substituents

Hydroxy fatty acid
Heterocyclic fatty acid
Unsaturated fatty acid
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic heteromonocyclic compound

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	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	0.59	ChemAxon
pKa (Strongest Acidic)	4.47	ChemAxon
pKa (Strongest Basic)	-2.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	51.95 m³·mol⁻¹	ChemAxon
Polarizability	21.13 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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

DOI: 10.1002/cbdv.202301512

Showing NP-Card for Phomalone B (NP0332113)

MOL for NP0332113 (Phomalone B)

3D MOL for NP0332113 (Phomalone B)

3D SDF for NP0332113 (Phomalone B)

3D-SDF for NP0332113 (Phomalone B)

PDB for NP0332113 (Phomalone B)

3D PDB for NP0332113 (Phomalone B)

SMILES for NP0332113 (Phomalone B)

INCHI for NP0332113 (Phomalone B)

Structure for NP0332113 (Phomalone B)

3D Structure for NP0332113 (Phomalone B)