NP-MRD: Showing NP-Card for (4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid (NP0302256)

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Record Information

Version

2.0

Created at

2022-09-10 15:40:57 UTC

Updated at

2022-09-10 15:40:57 UTC

NP-MRD ID

NP0302256

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid

Description

(4R)-4-[(2S,5S,7R,9S,11R,14S,15R)-5,9-dihydroxy-2,6,6,11,15-pentamethyl-12,17-dioxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadec-1(10)-en-14-yl]-4-hydroxypentanoic acid belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Based on a literature review very few articles have been published on (4R)-4-[(2S,5S,7R,9S,11R,14S,15R)-5,9-dihydroxy-2,6,6,11,15-pentamethyl-12,17-dioxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadec-1(10)-en-14-yl]-4-hydroxypentanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102217402D          

 34 37  0  0  1  0            999 V2000
    4.7094    0.3328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309102217402D          

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  8 15  1  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  6  0  0  0
 22 23  1  1  0  0  0
 22 24  1  1  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 21 30  1  0  0  0  0
 16 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 10 33  1  0  0  0  0
 33 34  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0302256

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@](O)(CCC(O)=O)[C@H]1CC(=O)[C@@]2(C)C3=C(C(=O)C[C@]12C)[C@@]1(C)CC[C@H](O)C(C)(C)[C@@H]1C[C@@H]3O

> <INCHI_IDENTIFIER>
InChI=1S/C27H40O7/c1-23(2)16-11-14(28)22-21(24(16,3)9-7-18(23)30)15(29)13-25(4)17(12-19(31)27(22,25)6)26(5,34)10-8-20(32)33/h14,16-18,28,30,34H,7-13H2,1-6H3,(H,32,33)/t14-,16-,17-,18-,24-,25+,26+,27-/m0/s1

> <INCHI_KEY>
KHMZFMPQPFGSOS-GACXBPKFSA-N

> <FORMULA>
C27H40O7

> <MOLECULAR_WEIGHT>
476.61

> <EXACT_MASS>
476.277403628

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
52.26677488636265

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R)-4-[(2S,5S,7R,9S,11R,14S,15R)-5,9-dihydroxy-2,6,6,11,15-pentamethyl-12,17-dioxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-1(10)-en-14-yl]-4-hydroxypentanoic acid

> <JCHEM_LOGP>
1.7352687963333349

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.316886743941616

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.132736620824617

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8070095175711619

> <JCHEM_POLAR_SURFACE_AREA>
132.13000000000002

> <JCHEM_REFRACTIVITY>
126.19349999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R)-4-[(2S,5S,7R,9S,11R,14S,15R)-5,9-dihydroxy-2,6,6,11,15-pentamethyl-12,17-dioxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-1(10)-en-14-yl]-4-hydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       8.791   0.621   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.459   1.394   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.929  -0.051   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.452   2.572   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       9.968   2.301   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.929   4.020   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.413   4.291   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.420   3.114   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.897   4.562   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.904   3.385   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.911   2.208   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.434   0.759   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.442  -0.418   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.950   0.488   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.943   1.666   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.395   2.479   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.764   0.984   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.179   1.534   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.230  -0.006   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -1.095   2.398   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.667   3.877   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.612   5.093   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.396   6.038   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.828   4.148   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.557   6.309   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.083   6.098   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.028   7.314   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -6.554   7.103   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -4.448   8.740   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       0.872   3.927   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.200   5.313   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.865   5.104   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.381   4.833   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       4.374   6.011   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4   15                                             
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   15                                             
CONECT    9    8                                                            
CONECT   10    8   11   33                                                  
CONECT   11   10   12   16                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    2    8                                                  
CONECT   16   11   17   18   30                                             
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   30                                                  
CONECT   22   21   23   24   25                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   22   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   21   16   31   32                                             
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   10   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Value	Source
(4R)-4-[(2S,5S,7R,9S,11R,14S,15R)-5,9-Dihydroxy-2,6,6,11,15-pentamethyl-12,17-dioxotetracyclo[8.7.0.0,.0,]heptadec-1(10)-en-14-yl]-4-hydroxypentanoate	Generator

Chemical Formula

C₂₇H₄₀O₇

Average Mass

476.6100 Da

Monoisotopic Mass

476.27740 Da

IUPAC Name

(4R)-4-[(2S,5S,7R,9S,11R,14S,15R)-5,9-dihydroxy-2,6,6,11,15-pentamethyl-12,17-dioxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-1(10)-en-14-yl]-4-hydroxypentanoic acid

Traditional Name

(4R)-4-[(2S,5S,7R,9S,11R,14S,15R)-5,9-dihydroxy-2,6,6,11,15-pentamethyl-12,17-dioxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-1(10)-en-14-yl]-4-hydroxypentanoic acid

CAS Registry Number

Not Available

SMILES

C[C@@](O)(CCC(O)=O)[C@H]1CC(=O)[C@@]2(C)C3=C(C(=O)C[C@]12C)[C@@]1(C)CC[C@H](O)C(C)(C)[C@@H]1C[C@@H]3O

InChI Identifier

InChI=1S/C27H40O7/c1-23(2)16-11-14(28)22-21(24(16,3)9-7-18(23)30)15(29)13-25(4)17(12-19(31)27(22,25)6)26(5,34)10-8-20(32)33/h14,16-18,28,30,34H,7-13H2,1-6H3,(H,32,33)/t14-,16-,17-,18-,24-,25+,26+,27-/m0/s1

InChI Key

KHMZFMPQPFGSOS-GACXBPKFSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Trihydroxy bile acid, alcohol, or derivatives
Hydroxy bile acid, alcohol, or derivatives
Bile acid, alcohol, or derivatives
20-hydroxysteroid
14-alpha-methylsteroid
7-hydroxysteroid
7-alpha-hydroxysteroid
3-beta-hydroxysteroid
Oxosteroid
15-oxosteroid
11-oxosteroid
Hydroxysteroid
3-hydroxysteroid
Steroid
Cyclohexenone
Short-chain hydroxy acid
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	1.74	ChemAxon
pKa (Strongest Acidic)	4.13	ChemAxon
pKa (Strongest Basic)	-0.81	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.19 m³·mol⁻¹	ChemAxon
Polarizability	52.27 Å³	ChemAxon
Number of Rings	4	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

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

163011039

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid (NP0302256)

MOL for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

3D MOL for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

3D SDF for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

3D-SDF for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

PDB for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

3D PDB for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

SMILES for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

INCHI for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

Structure for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)

3D Structure for NP0302256 ((4r)-4-[(1s,3ar,4s,5ar,7s,9as,11ar)-4,7-dihydroxy-3a,6,6,9a,11a-pentamethyl-3,10-dioxo-1h,2h,4h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-4-hydroxypentanoic acid)