NP-MRD: Showing NP-Card for Obscuraminol D (NP0138965)

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Record Information

Version

1.0

Created at

2022-06-29 19:33:38 UTC

Updated at

2022-06-29 19:33:38 UTC

NP-MRD ID

NP0138965

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Obscuraminol D

Description

Obscuraminol d belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom. Thus, obscuraminol D is considered to be a sphingoid base. It was first documented in 1993 (PMID: 35862567). Based on a literature review a significant number of articles have been published on Obscuraminol d (PMID: 35863877) (PMID: 35863750) (PMID: 35863742) (PMID: 35863720) (PMID: 35863712) (PMID: 35863704).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 51 50  0  0  0  0  0  0  0  0999 V2000
    7.5322    0.2207   -1.1394 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9998    1.4281   -0.3914 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9779    0.9390    0.5980 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8766    0.2469   -0.1914 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8577   -0.2380    0.8270 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7438   -0.9347    0.0657 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7694   -1.3963    1.0644 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5255   -0.9774    1.0511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0389   -0.0418    0.0941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1879   -0.6609   -0.6958 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3202   -1.1096    0.1530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9869   -0.0775    0.9686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6051    1.0669    0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6943    0.6967   -0.7116 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1911   -0.1289   -1.6885 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8887    0.0782   -0.0161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.9464   -0.1789   -1.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3473    1.0175    0.9919 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0808    0.1610   -2.1519 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6312    0.3509   -1.1993 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2969   -0.7248   -0.5865 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7808    1.9771    0.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4557    2.0911   -1.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4823    1.7699    1.1462 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3855    0.1857    1.2989 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3905    0.9344   -0.9109 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2602   -0.6624   -0.6988 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5021    0.6191    1.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3136   -0.9594    1.5108 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2307   -1.8682   -0.3556 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3738   -0.3882   -0.7848 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0623   -2.1086    1.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1729   -1.3540    1.8268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4677    0.8484    0.6645 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6349    0.4225   -0.6351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7537   -1.5629   -1.1892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4387    0.0432   -1.4886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0155   -1.7136   -0.4649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8958   -1.8657    0.8819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8241   -0.6000    1.5254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2999    0.2453    1.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9030    1.7283   -0.2694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0931    1.7128    1.0414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9916    1.6489   -1.2147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8159   -0.7802   -2.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6294   -0.8539    0.5081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8277    0.5761   -1.8676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7508   -1.1707   -1.5342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9697   -0.2057   -0.6538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3306    0.7078    1.2536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7770    0.8459    1.8501 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  0
  2 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  4 27  1  0
  5 28  1  0
  5 29  1  0
  6 30  1  0
  6 31  1  0
  7 32  1  0
  8 33  1  0
  9 34  1  0
  9 35  1  0
 10 36  1  0
 10 37  1  0
 11 38  1  0
 11 39  1  0
 12 40  1  0
 12 41  1  0
 13 42  1  0
 13 43  1  0
 14 44  1  6
 15 45  1  0
 16 46  1  1
 17 47  1  0
 17 48  1  0
 17 49  1  0
 18 50  1  0
 18 51  1  0
M  END


  Mrv1652306292221332D          

 18 17  0  0  1  0            999 V2000
   -1.2888    0.9059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5743    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1401    0.9059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5691    0.9059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    0.9059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 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
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  6  0  0  0
 14 18  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0138965

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCC\C=C/CCCCC[C@@H](O)[C@H](C)N

> <INCHI_IDENTIFIER>
InChI=1S/C16H33NO/c1-3-4-5-6-7-8-9-10-11-12-13-14-16(18)15(2)17/h8-9,15-16,18H,3-7,10-14,17H2,1-2H3/b9-8-/t15-,16+/m0/s1

> <INCHI_KEY>
SHEYJRIILVVUIW-LWULTOEVSA-N

> <FORMULA>
C16H33NO

> <MOLECULAR_WEIGHT>
255.446

> <EXACT_MASS>
255.256214687

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
33.698661824486564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R,9Z)-2-aminohexadec-9-en-3-ol

> <ALOGPS_LOGP>
5.21

> <JCHEM_LOGP>
4.568445225333334

> <ALOGPS_LOGS>
-5.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.620676804177457

> <JCHEM_PKA_STRONGEST_BASIC>
9.832643159623604

> <JCHEM_POLAR_SURFACE_AREA>
46.25

> <JCHEM_REFRACTIVITY>
81.3003

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.89e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,9Z)-2-aminohexadec-9-en-3-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0      -2.406   1.691   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.072   2.461   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.262   1.691   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.595   2.461   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.929   1.691   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.263   2.461   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.596   1.691   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.930   2.461   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      16.266   4.771   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      14.932   2.461   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      13.598   6.311   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   14                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₃₃NO

Average Mass

255.4460 Da

Monoisotopic Mass

255.25621 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CCCCCC\C=C/CCCCC[C@@H](O)[C@H](C)N

InChI Identifier

InChI=1S/C16H33NO/c1-3-4-5-6-7-8-9-10-11-12-13-14-16(18)15(2)17/h8-9,15-16,18H,3-7,10-14,17H2,1-2H3/b9-8-/t15-,16+/m0/s1

InChI Key

SHEYJRIILVVUIW-LWULTOEVSA-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 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

1,2-aminoalcohols

Alternative Parents

Substituents

Secondary alcohol
1,2-aminoalcohol
Organic oxygen compound
Hydrocarbon derivative
Primary amine
Organooxygen compound
Primary aliphatic amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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

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

107561923

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101101127

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Morales Corado JA, Lee CU, Enns GM: Carnitine-Acylcarnitine Translocase Deficiency. 1993. [PubMed:35862567 ]
Jessup WH, Wiegand J, Delbridge-Perry M, MacAvoy SE, Connaughton VP: Developmental effects of siloxane exposure in zebrafish: A comparison study using laboratory-mixed and environmental water samples. J Appl Toxicol. 2022 Dec;42(12):1986-2004. doi: 10.1002/jat.4369. Epub 2022 Jul 29. [PubMed:35863877 ]
Qing Z, Mao P, Wang T, Zhai H: Correction to "Asymmetric Total Syntheses of Cephalotane-Type Diterpenoids Cephanolides A-D". J Am Chem Soc. 2022 Aug 3;144(30):13982. doi: 10.1021/jacs.2c07171. Epub 2022 Jul 21. [PubMed:35863750 ]
Wu S, Zhang H, Gao C, Chen J, Li H, Meng Z, Bai J, Shen Q, Wu H, Yin T: Hyperglycemia Enhances Immunosuppression and Aerobic Glycolysis of Pancreatic Cancer Through Upregulating Bmi1-UPF1-HK2 Pathway. Cell Mol Gastroenterol Hepatol. 2022;14(5):1146-1165. doi: 10.1016/j.jcmgh.2022.07.008. Epub 2022 Jul 19. [PubMed:35863742 ]
Wang H, Chen J, Zhao J, Li H, Wei X, Liu J: Improved thermostability of D-allulose 3-epimerase from Clostridium bolteae ATCC BAA-613 by proline residue substitution. Protein Expr Purif. 2022 Nov;199:106145. doi: 10.1016/j.pep.2022.106145. Epub 2022 Jul 19. [PubMed:35863720 ]
Sur R, Kley C, Sittig S: Field leaching study - Inverse estimation of degradation and sorption parameters for a mobile soil metabolite and its pesticide parent. Environ Pollut. 2022 Oct 1;310:119794. doi: 10.1016/j.envpol.2022.119794. Epub 2022 Jul 18. [PubMed:35863712 ]
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Showing NP-Card for Obscuraminol D (NP0138965)

MOL for NP0138965 (Obscuraminol D)

3D MOL for NP0138965 (Obscuraminol D)

3D SDF for NP0138965 (Obscuraminol D)

3D-SDF for NP0138965 (Obscuraminol D)

PDB for NP0138965 (Obscuraminol D)

3D PDB for NP0138965 (Obscuraminol D)

SMILES for NP0138965 (Obscuraminol D)

INCHI for NP0138965 (Obscuraminol D)

Structure for NP0138965 (Obscuraminol D)

3D Structure for NP0138965 (Obscuraminol D)