NP-MRD: Showing NP-Card for (+)-(2S',3'R)-3-Hydroxymarmesin (NP0063151)

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Record Information

Version

1.0

Created at

2022-04-28 07:37:30 UTC

Updated at

2022-04-28 07:37:30 UTC

NP-MRD ID

NP0063151

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-(2S',3'R)-3-Hydroxymarmesin

Description

Smyrindiol belongs to the class of organic compounds known as psoralens. These are organic compounds containing a psoralen moiety, which consists of a furan fused to a chromenone to for 7H-furo[3,2-g]chromen-7-one. (+)-(2S',3'R)-3-Hydroxymarmesin is found in Brosimum gaudichaudii, Dorstenia brasiliensis , Dorstenia turbinata and Smyrniopsis aucheri. It was first documented in 2005 (PMID: 15730299). Based on a literature review a small amount of articles have been published on Smyrindiol (PMID: 23234138) (PMID: 23019438).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 35  0  0  0  0  0  0  0  0999 V2000
   -3.5421   -0.7008   -0.6455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0182    0.6733   -0.3957 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7134    1.2478    0.8069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3521    1.4684   -1.4899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5388    0.7413   -0.1993 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0774   -0.0298    0.8883 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3118   -0.1352    0.6728 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3799   -0.3171    1.5372 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6952   -0.3916    1.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7034   -0.5620    1.8809 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9268   -0.6276    1.4160 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9313   -0.7946    2.1876 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2179   -0.5221    0.0727 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1852   -0.3406   -0.8205 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8995   -0.2768   -0.2795 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8657   -0.0946   -1.1793 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5848   -0.0278   -0.6746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7536    0.1561   -1.3366 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1808   -1.1209   -1.6914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6366   -0.6891   -0.3645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5161   -1.0230   -1.6976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0818   -1.4409    0.0529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6861    1.7374    0.5544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9681    0.4458    1.5323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0746    1.9980    1.3220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5583    0.9720   -2.2989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2312    1.7757   -0.0503 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2333   -0.4089    2.6072 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2314   -0.5765   -0.3119 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3261   -0.2487   -1.8866 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0184   -0.0037   -2.2458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6713    0.8317   -2.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9101   -1.7154   -0.9311 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  6
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7 17  2  0
 17 16  1  0
 16 15  2  0
 15 14  1  0
 14 13  2  0
 13 11  1  0
 11 12  2  0
 11 10  1  0
 10  9  1  0
  9  8  2  0
 17 18  1  0
 18 19  1  0
 18  5  1  0
  8  7  1  0
  9 15  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  5 27  1  1
 16 31  1  0
 14 30  1  0
 13 29  1  0
  8 28  1  0
 18 32  1  6
 19 33  1  0
M  END


  Mrv1652304282209372D          

 19 21  0  0  1  0            999 V2000
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    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  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    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
    0.0000   -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 O   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
    3.6425    1.0799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1274    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6425   -0.2549    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8974   -1.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7774    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    1.2375    0.0000 C   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  1 14  1  0  0  0  0
 14 15  1  6  0  0  0
 13 16  1  6  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 16 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0063151

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(O)[C@H]1OC2=C(C=C3C=CC(=O)OC3=C2)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H14O5/c1-14(2,17)13-12(16)8-5-7-3-4-11(15)18-9(7)6-10(8)19-13/h3-6,12-13,16-17H,1-2H3/t12-,13+/m1/s1

> <INCHI_KEY>
AIQSGHBQRRSBCN-OLZOCXBDSA-N

> <FORMULA>
C14H14O5

> <MOLECULAR_WEIGHT>
262.261

> <EXACT_MASS>
262.084123551

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
26.434193857488196

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R)-3-hydroxy-2-(2-hydroxypropan-2-yl)-2H,3H,7H-furo[3,2-g]chromen-7-one

> <ALOGPS_LOGP>
1.30

> <JCHEM_LOGP>
0.8133974599999996

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.344612334701132

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.055497989177642

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1430297624223256

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
67.5484

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.44e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R)-3-hydroxy-2-(2-hydroxypropan-2-yl)-2H,3H-furo[3,2-g]chromen-7-one

> <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       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   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       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.799   2.016   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       7.705   0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.799  -0.476   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.275  -1.941   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       9.245   0.770   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      10.785   0.770   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       9.245  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.245   2.310   0.000  0.00  0.00           C+0
CONECT    1    2    6   14                                                  
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4                                                       
CONECT   12    2   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13    1   15                                                  
CONECT   15   14                                                            
CONECT   16   13   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₁₄O₅

Average Mass

262.2610 Da

Monoisotopic Mass

262.08412 Da

IUPAC Name

(2S,3R)-3-hydroxy-2-(2-hydroxypropan-2-yl)-2H,3H,7H-furo[3,2-g]chromen-7-one

Traditional Name

(2S,3R)-3-hydroxy-2-(2-hydroxypropan-2-yl)-2H,3H-furo[3,2-g]chromen-7-one

CAS Registry Number

Not Available

SMILES

CC(C)(O)[C@H]1OC2=C(C=C3C=CC(=O)OC3=C2)[C@H]1O

InChI Identifier

InChI=1S/C14H14O5/c1-14(2,17)13-12(16)8-5-7-3-4-11(15)18-9(7)6-10(8)19-13/h3-6,12-13,16-17H,1-2H3/t12-,13+/m1/s1

InChI Key

AIQSGHBQRRSBCN-OLZOCXBDSA-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, 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

Not Available

Species

Species of Origin

Species Name	Source	Reference
Brosimum gaudichaudii	Plant	KNApSAcK
Dorstenia brasiliensis	Plant	KNApSAcK
Dorstenia turbinata	Plant	KNApSAcK
Smyrniopsis aucheri	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as psoralens. These are organic compounds containing a psoralen moiety, which consists of a furan fused to a chromenone to for 7H-furo[3,2-g]chromen-7-one.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Furanocoumarins

Direct Parent

Psoralens

Alternative Parents

Substituents

Psoralen
Benzopyran
1-benzopyran
Coumaran
Alkyl aryl ether
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Tertiary alcohol
Lactone
Secondary alcohol
Oxacycle
Ether
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	1.3	ALOGPS
logP	0.81	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	13.06	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	67.55 m³·mol⁻¹	ChemAxon
Polarizability	26.43 Å³	ChemAxon
Number of Rings	3	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

C00019918

Chemspider ID

52085837

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

92261439

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zou Y, Lobera M, Snider BB: Synthesis of 2,3-dihydro-3-hydroxy-2-hydroxylalkylbenzofurans from epoxy aldehydes. One-step syntheses of brosimacutin G, vaginidiol, vaginol, smyrindiol, xanthoarnol, and Avicenol A. Biomimetic syntheses of angelicin and psoralen. J Org Chem. 2005 Mar 4;70(5):1761-70. doi: 10.1021/jo047974k. [PubMed:15730299 ]
Zhao A, Yang X, Yang X, Liu J, Wang Q, Wang W: [A new natural product from root of Angelica dahurica cv. Qibaizhi]. Zhongguo Zhong Yao Za Zhi. 2012 Aug;37(16):2400-7. [PubMed:23234138 ]
Enders D, Fronert J, Bisschops T, Boeck F: Asymmetric total synthesis of smyrindiol employing an organocatalytic aldol key step. Beilstein J Org Chem. 2012;8:1112-7. doi: 10.3762/bjoc.8.123. Epub 2012 Jul 18. [PubMed:23019438 ]

Showing NP-Card for (+)-(2S',3'R)-3-Hydroxymarmesin (NP0063151)

MOL for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

3D MOL for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

3D SDF for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

3D-SDF for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

PDB for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

3D PDB for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

SMILES for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

INCHI for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

Structure for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)

3D Structure for NP0063151 ((+)-(2S',3'R)-3-Hydroxymarmesin)