NP-MRD: Showing NP-Card for Rhapontin (NP0338076)

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Record Information

Version

2.0

Created at

2024-09-11 13:43:51 UTC

Updated at

2024-09-11 13:43:51 UTC

NP-MRD ID

NP0338076

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rhapontin

Description

Rhapontin was first documented in 2020 (PMID: 35520676). Based on a literature review a small amount of articles have been published on Rhapontin (PMID: 34254908) (PMID: 38919748) (PMID: 37295190) (PMID: 38757037).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05262316162D          

 30 32  0  0  0  0            999 V2000
   -0.3562    0.2069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562   -0.6181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -1.0306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0698   -0.6181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0698    0.2069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574    0.6180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712   -1.0306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712   -1.8571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562   -2.2709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -1.8571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562   -3.0960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -3.5085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0698   -3.0960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0698   -2.2709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574    1.4430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7848   -1.0306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7848   -3.5085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4999   -3.0960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562    1.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562    2.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    3.0946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848    2.6806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848    1.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    1.4430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    0.6180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4999    1.4430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4999    3.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    3.9196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848    4.3336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -4.3336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4 16  1  0  0  0  0
  5  6  2  0  0  0  0
  6 15  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
 10 14  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 30  1  0  0  0  0
 13 14  2  0  0  0  0
 13 17  1  0  0  0  0
 15 19  1  0  0  0  0
 17 18  1  0  0  0  0
 19 20  1  0  0  0  0
 19 24  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 28  1  0  0  0  0
 22 23  1  0  0  0  0
 22 27  1  0  0  0  0
 23 24  1  0  0  0  0
 23 26  1  0  0  0  0
 24 25  1  0  0  0  0
 28 29  1  0  0  0  0
M  END


  Mrv2104 05262316162D          

 30 32  0  0  0  0            999 V2000
   -0.3562    0.2069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562   -0.6181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -1.0306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0698   -0.6181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0698    0.2069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574    0.6180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712   -1.0306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712   -1.8571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562   -2.2709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -1.8571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562   -3.0960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -3.5085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0698   -3.0960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0698   -2.2709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574    1.4430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7848   -1.0306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7848   -3.5085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4999   -3.0960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562    1.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562    2.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    3.0946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848    2.6806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848    1.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    1.4430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    0.6180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4999    1.4430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4999    3.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    3.9196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848    4.3336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -4.3336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4 16  1  0  0  0  0
  5  6  2  0  0  0  0
  6 15  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
 10 14  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 30  1  0  0  0  0
 13 14  2  0  0  0  0
 13 17  1  0  0  0  0
 15 19  1  0  0  0  0
 17 18  1  0  0  0  0
 19 20  1  0  0  0  0
 19 24  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 28  1  0  0  0  0
 22 23  1  0  0  0  0
 22 27  1  0  0  0  0
 23 24  1  0  0  0  0
 23 26  1  0  0  0  0
 24 25  1  0  0  0  0
 28 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0338076

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(\C=C/C2=CC(OC3OC(CO)C(O)C(O)C3O)=CC(O)=C2)C=C1O

> <INCHI_IDENTIFIER>
InChI=1/C21H24O9/c1-28-16-5-4-11(8-15(16)24)2-3-12-6-13(23)9-14(7-12)29-21-20(27)19(26)18(25)17(10-22)30-21/h2-9,17-27H,10H2,1H3/b3-2-

> <INCHI_KEY>
GKAJCVFOJGXVIA-IHWYPQMZNA-N

> <FORMULA>
C21H24O9

> <MOLECULAR_WEIGHT>
420.414

> <EXACT_MASS>
420.142032353

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
42.333847616536744

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{3-hydroxy-5-[(1Z)-2-(3-hydroxy-4-methoxyphenyl)ethenyl]phenoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
0.9766515273333334

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.95643046969659

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.21091603590187

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092343730565

> <JCHEM_POLAR_SURFACE_AREA>
149.07

> <JCHEM_REFRACTIVITY>
106.06309999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-{3-hydroxy-5-[(1Z)-2-(3-hydroxy-4-methoxyphenyl)ethenyl]phenoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  C   UNK     0      -0.665   0.386   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.665  -1.154   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.667  -1.924   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.997  -1.154   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.997   0.386   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.667   1.154   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.000  -1.924   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.000  -3.467   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.665  -4.239   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.667  -3.467   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.665  -5.779   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.667  -6.549   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.997  -5.779   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.997  -4.239   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.667   2.694   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.332  -1.924   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.332  -6.549   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.666  -5.779   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.665   3.464   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.665   5.004   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -2.000   5.777   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.332   5.004   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.332   3.464   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.000   2.694   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -2.000   1.154   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -4.666   2.694   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -4.666   5.777   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.000   7.317   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -3.332   8.089   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.667  -8.089   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   16                                                  
CONECT    5    4    6                                                       
CONECT    6    1    5   15                                                  
CONECT    7    2    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9   14                                                       
CONECT   11    9   12                                                       
CONECT   12   11   13   30                                                  
CONECT   13   12   14   17                                                  
CONECT   14   10   13                                                       
CONECT   15    6   19                                                       
CONECT   16    4                                                            
CONECT   17   13   18                                                       
CONECT   18   17                                                            
CONECT   19   15   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   28                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24   26                                                  
CONECT   24   19   23   25                                                  
CONECT   25   24                                                            
CONECT   26   23                                                            
CONECT   27   22                                                            
CONECT   28   21   29                                                       
CONECT   29   28                                                            
CONECT   30   12                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₂₄O₉

Average Mass

420.4140 Da

Monoisotopic Mass

420.14203 Da

IUPAC Name

2-{3-hydroxy-5-[(1Z)-2-(3-hydroxy-4-methoxyphenyl)ethenyl]phenoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-{3-hydroxy-5-[(1Z)-2-(3-hydroxy-4-methoxyphenyl)ethenyl]phenoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

COC1=CC=C(\C=C/C2=CC(OC3OC(CO)C(O)C(O)C3O)=CC(O)=C2)C=C1O

InChI Identifier

InChI=1/C21H24O9/c1-28-16-5-4-11(8-15(16)24)2-3-12-6-13(23)9-14(7-12)29-21-20(27)19(26)18(25)17(10-22)30-21/h2-9,17-27H,10H2,1H3/b3-2-

InChI Key

GKAJCVFOJGXVIA-IHWYPQMZNA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Classification

Not classified

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	0.98	ChemAxon
pKa (Strongest Acidic)	9.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	149.07 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	106.06 m³·mol⁻¹	ChemAxon
Polarizability	42.33 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

Rhaponticin

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ouyang X, Li X, Liu J, Liu Y, Xie Y, Du Z, Xie H, Chen B, Lu W, Chen D: Structure-activity relationship and mechanism of four monostilbenes with respect to ferroptosis inhibition. RSC Adv. 2020 Aug 21;10(52):31171-31179. doi: 10.1039/d0ra04896h. eCollection 2020 Aug 21. [PubMed:35520676 ]
Rehman A, Ashfaq UA, Javed MR, Shahid F, Noor F, Aslam S: The Screening of Phytochemicals Against NS5 Polymerase to Treat Zika Virus Infection: Integrated Computational Based Approach. Comb Chem High Throughput Screen. 2022;25(4):738-751. doi: 10.2174/1386207324666210712091920. [PubMed:34254908 ]
Zeng Q, Hu H, Huang Z, Guo A, Lu S, Tong W, Zhang Z, Shen T: Active and machine learning-enhanced discovery of new FGFR3 inhibitor, Rhapontin, through virtual screening of receptor structures and anti-cancer activity assessment. Front Mol Biosci. 2024 Jun 11;11:1413214. doi: 10.3389/fmolb.2024.1413214. eCollection 2024. [PubMed:38919748 ]
Liu L, Liu H, Yan H, Guo H, Bai L: Separation and purification of glycosides from medicinal plants based on strong polar separation medium with online closed-loop mode. J Pharm Biomed Anal. 2023 Sep 20;234:115508. doi: 10.1016/j.jpba.2023.115508. Epub 2023 Jun 7. [PubMed:37295190 ]
AlAjmi MF, Azhar A, Hasan S, Alshabr AZ, Hussain A, Rehman MT: Identification of natural compounds (proanthocyanidin and rhapontin) as high-affinity inhibitors of SARS-CoV-2 Mpro and PLpro using computational strategies. Arch Med Sci. 2021 Mar 20;20(2):567-581. doi: 10.5114/aoms/133706. eCollection 2024. [PubMed:38757037 ]

Showing NP-Card for Rhapontin (NP0338076)

MOL for NP0338076 (Rhapontin)

3D MOL for NP0338076 (Rhapontin)

3D SDF for NP0338076 (Rhapontin)

3D-SDF for NP0338076 (Rhapontin)

PDB for NP0338076 (Rhapontin)

3D PDB for NP0338076 (Rhapontin)

SMILES for NP0338076 (Rhapontin)

INCHI for NP0338076 (Rhapontin)

Structure for NP0338076 (Rhapontin)

3D Structure for NP0338076 (Rhapontin)