NP-MRD: Showing NP-Card for 11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol (NP0297459)

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Record Information

Version

2.0

Created at

2022-09-10 07:49:09 UTC

Updated at

2022-09-10 07:49:09 UTC

NP-MRD ID

NP0297459

Secondary Accession Numbers

None

Natural Product Identification

Common Name

11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol

Description

14-(Hydroxymethyl)-6-(2-hydroxypropan-2-yl)-1,2,9,18,18-pentamethylpentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]Henicosane-12,15-diol belongs to the class of organic compounds known as hopanoids. These are terpenoids containing hopane skeleton(A'-Neogammacerane), a pentacyclic structure with four cyclohexane rings and one cyclopentane ring (and often, a side chain emerging from C30). 11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol is found in Cheiropleuria bicuspis. 14-(Hydroxymethyl)-6-(2-hydroxypropan-2-yl)-1,2,9,18,18-pentamethylpentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]Henicosane-12,15-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004241504122D          

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M  END

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M  END


  Mrv1533004241504122D          

 34 38  0  0  0  0            999 V2000
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    1.1378   -0.2956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3129   -0.3082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4580   -0.6021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4685   -1.1184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1104    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2912    1.1206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1161    1.1332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5176    1.8538    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5394    0.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9410    1.1457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0147    1.9674    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
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  8 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 13 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 19 32  1  0  0  0  0
 24 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0297459

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(O)C1CCC2(C)C1CCC1(C)C2CC(O)C2C1(C)CCC1C(C)(C)CCC(O)C21CO

> <INCHI_IDENTIFIER>
InChI=1S/C30H52O4/c1-25(2)12-11-23(33)30(17-31)21(25)10-15-29(7)24(30)20(32)16-22-27(5)13-8-18(26(3,4)34)19(27)9-14-28(22,29)6/h18-24,31-34H,8-17H2,1-7H3

> <INCHI_KEY>
OEKDVCVHTSEFMM-UHFFFAOYSA-N

> <FORMULA>
C30H52O4

> <MOLECULAR_WEIGHT>
476.742

> <EXACT_MASS>
476.386560154

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
86

> <JCHEM_AVERAGE_POLARIZABILITY>
56.780811952463

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
14-(hydroxymethyl)-6-(2-hydroxypropan-2-yl)-1,2,9,18,18-pentamethylpentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosane-12,15-diol

> <ALOGPS_LOGP>
4.20

> <JCHEM_LOGP>
3.812995383333334

> <ALOGPS_LOGS>
-4.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.876731857535159

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.32683434026998

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8403453539236437

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
136.25709999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.28e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
14-(hydroxymethyl)-6-(2-hydroxypropan-2-yl)-1,2,9,18,18-pentamethylpentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosane-12,15-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0      11.471  -2.265   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.484  -1.105   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.644  -2.118   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      13.497   0.055   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      11.324  -0.092   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.462   1.442   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.046   2.047   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.033   0.887   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.385   2.284   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.823  -0.435   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.073  -1.780   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.534  -1.803   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.743  -0.482   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.994  -1.827   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.493   0.864   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.703   2.185   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.163   2.162   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.373   3.484   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.413   0.817   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.204  -0.505   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.066  -2.039   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.454  -1.850   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.914  -1.874   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.124  -0.552   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.584  -0.575   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.855  -1.124   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.875  -2.088   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.206   0.747   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.543   2.092   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.083   2.115   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       2.833   3.460   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       2.874   0.793   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.623   2.139   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       3.761   3.672   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   15                                             
CONECT    9    8                                                            
CONECT   10    8    5   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15   20                                             
CONECT   14   13                                                            
CONECT   15   13    8   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   32                                                  
CONECT   20   19   13   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   32                                                  
CONECT   25   24   26   27   28                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   25   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   19   24   33                                             
CONECT   33   32   34                                                       
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₅₂O₄

Average Mass

476.7420 Da

Monoisotopic Mass

476.38656 Da

IUPAC Name

14-(hydroxymethyl)-6-(2-hydroxypropan-2-yl)-1,2,9,18,18-pentamethylpentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosane-12,15-diol

Traditional Name

14-(hydroxymethyl)-6-(2-hydroxypropan-2-yl)-1,2,9,18,18-pentamethylpentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosane-12,15-diol

CAS Registry Number

Not Available

SMILES

CC(C)(O)C1CCC2(C)C1CCC1(C)C2CC(O)C2C1(C)CCC1C(C)(C)CCC(O)C21CO

InChI Identifier

InChI=1S/C30H52O4/c1-25(2)12-11-23(33)30(17-31)21(25)10-15-29(7)24(30)20(32)16-22-27(5)13-8-18(26(3,4)34)19(27)9-14-28(22,29)6/h18-24,31-34H,8-17H2,1-7H3

InChI Key

OEKDVCVHTSEFMM-UHFFFAOYSA-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
Cheiropleuria bicuspis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hopanoids. These are terpenoids containing hopane skeleton(A'-Neogammacerane), a pentacyclic structure with four cyclohexane rings and one cyclopentane ring (and often, a side chain emerging from C30).

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Hopanoids

Direct Parent

Hopanoids

Alternative Parents

Substituents

Triterpenoid
Hopane-skeleton
20-hydroxysteroid
Hydroxysteroid
6-hydroxysteroid
Steroid
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
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	4.2	ALOGPS
logP	3.81	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	14.33	ChemAxon
pKa (Strongest Basic)	-0.84	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	2	ChemAxon
Refractivity	136.26 m³·mol⁻¹	ChemAxon
Polarizability	56.78 Å³	ChemAxon
Number of Rings	5	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

13942969

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol (NP0297459)

MOL for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

3D MOL for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

3D SDF for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

3D-SDF for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

PDB for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

3D PDB for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

SMILES for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

INCHI for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

Structure for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)

3D Structure for NP0297459 (11a-(hydroxymethyl)-3-(2-hydroxypropan-2-yl)-5a,5b,8,8,13b-pentamethyl-hexadecahydrocyclopenta[a]chrysene-11,12-diol)