NP-MRD: Showing NP-Card for [(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid (NP0326237)

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Record Information

Version

2.0

Created at

2022-09-12 07:37:04 UTC

Updated at

2022-09-12 07:37:04 UTC

NP-MRD ID

NP0326237

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid

Description

Kapurimycin A3 belongs to the class of organic compounds known as naphthopyranones. Naphthopyranones are compounds containing a naphthopyran skeleton where a ring carbon bears a carboxylic acid group. Naphthtopyran is made up of the pyran ring fused to a naphthalene ring system. [(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid was first documented in 1991 (PMID: 30260325). Based on a literature review a small amount of articles have been published on Kapurimycin A3 (PMID: 9585982) (PMID: 8534399) (PMID: 8451767) (PMID: 1842103).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122209372D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309122209372D          

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M  END
> <DATABASE_ID>
NP0326237

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C/[C@H]1O[C@]1(C)C1=CC(=O)C2=C(O1)C1=C(O)C3=C(C=C1C=C2CC(O)=O)[C@H](CCC3=O)OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H24O9/c1-4-5-19-27(3,36-19)20-11-17(30)22-14(10-21(31)32)8-13-9-15-18(34-12(2)28)7-6-16(29)24(15)25(33)23(13)26(22)35-20/h4-5,8-9,11,18-19,33H,6-7,10H2,1-3H3,(H,31,32)/b5-4-/t18-,19+,27-/m0/s1

> <INCHI_KEY>
GMKMVBAGONGKOV-ANGZKDRVSA-N

> <FORMULA>
C27H24O9

> <MOLECULAR_WEIGHT>
492.48

> <EXACT_MASS>
492.142032353

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
50.44866135764903

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(8S)-8-(acetyloxy)-12-hydroxy-2-[(2S,3R)-2-methyl-3-[(1Z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-8,9,10,11-tetrahydro-4H-1-oxatetraphen-5-yl]acetic acid

> <JCHEM_LOGP>
3.3060934093333323

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.292973794862078

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5021439260406644

> <JCHEM_PKA_STRONGEST_BASIC>
-4.270354148947288

> <JCHEM_POLAR_SURFACE_AREA>
139.73000000000002

> <JCHEM_REFRACTIVITY>
128.92229999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(8S)-8-(acetyloxy)-12-hydroxy-2-[(2S,3R)-2-methyl-3-[(1Z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8H-1-oxatetraphen-5-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      -9.036   1.024   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.194  -0.508   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -7.947  -1.411   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.541  -0.782   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -5.638   0.466   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -5.009  -0.940   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.469  -0.964   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.505  -2.395   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.513  -3.559   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.009  -5.014   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -6.017  -6.178   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -3.497  -5.305   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.993  -6.760   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.001  -7.924   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.497  -9.380   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.985  -9.671   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -4.505 -10.544   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -1.481  -7.051   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.472  -5.887   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.040  -6.178   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.048  -5.014   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.544  -3.559   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.032  -3.268   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -0.472  -1.813   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -0.977  -4.432   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.489  -4.141   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.993  -2.686   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.552  -2.395   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.048  -0.940   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.064  -2.686   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.568  -4.141   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.560  -5.305   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       4.064  -6.760   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       3.056  -7.924   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.560  -9.380   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       1.544  -7.633   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4    6                                                       
CONECT    6    5    4    7    8                                             
CONECT    7    6                                                            
CONECT    8    6    9   27                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   26                                                  
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   13   19                                                       
CONECT   19   18   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   32                                                  
CONECT   22   21   23   28                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   19   26                                                  
CONECT   26   25   12   27                                                  
CONECT   27   26    8                                                       
CONECT   28   22   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   21   33                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₂₄O₉

Average Mass

492.4800 Da

Monoisotopic Mass

492.14203 Da

IUPAC Name

2-[(8S)-8-(acetyloxy)-12-hydroxy-2-[(2S,3R)-2-methyl-3-[(1Z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-8,9,10,11-tetrahydro-4H-1-oxatetraphen-5-yl]acetic acid

Traditional Name

[(8S)-8-(acetyloxy)-12-hydroxy-2-[(2S,3R)-2-methyl-3-[(1Z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8H-1-oxatetraphen-5-yl]acetic acid

CAS Registry Number

Not Available

SMILES

C\C=C/[C@H]1O[C@]1(C)C1=CC(=O)C2=C(O1)C1=C(O)C3=C(C=C1C=C2CC(O)=O)[C@H](CCC3=O)OC(C)=O

InChI Identifier

InChI=1S/C27H24O9/c1-4-5-19-27(3,36-19)20-11-17(30)22-14(10-21(31)32)8-13-9-15-18(34-12(2)28)7-6-16(29)24(15)25(33)23(13)26(22)35-20/h4-5,8-9,11,18-19,33H,6-7,10H2,1-3H3,(H,31,32)/b5-4-/t18-,19+,27-/m0/s1

InChI Key

GMKMVBAGONGKOV-ANGZKDRVSA-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 naphthopyranones. Naphthopyranones are compounds containing a naphthopyran skeleton where a ring carbon bears a carboxylic acid group. Naphthtopyran is made up of the pyran ring fused to a naphthalene ring system.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Naphthopyrans

Sub Class

Naphthopyranones

Direct Parent

Naphthopyranones

Alternative Parents

Substituents

Naphthopyranone
1-naphthol
Chromone
Naphthalene
Benzopyran
Tetralin
1-benzopyran
Aryl alkyl ketone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
Pyranone
Dicarboxylic acid or derivatives
Pyran
Benzenoid
Heteroaromatic compound
Vinylogous acid
Carboxylic acid ester
Ketone
Carboxylic acid derivative
Carboxylic acid
Dialkyl ether
Oxacycle
Oxirane
Ether
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organic oxygen compound
Organooxygen 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	3.31	ChemAxon
pKa (Strongest Acidic)	3.5	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	139.73 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	128.92 m³·mol⁻¹	ChemAxon
Polarizability	50.45 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	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

4943075

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6438610

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Okamoto A, Nakatani K, Saito I: Studies on the mechanism of DNA sequence selective alkylation by kapurimycin A3 analogs. Nucleic Acids Symp Ser. 1997;(37):27-8. [PubMed:9585982 ]
Chan KL, Sugiyama H, Saito I, Hara M: NMR characterization of guanine DNA site alkylated by kapurimycin A3, an antitumour antibiotic from Streptomyces sp. Phytochemistry. 1995 Nov;40(5):1373-4. doi: 10.1016/0031-9422(95)00475-m. [PubMed:8534399 ]
Saito I: Chemistry of drug-induced DNA lesions. Toxicol Lett. 1993 Apr;67(1-3):3-15. doi: 10.1016/0378-4274(93)90042-v. [PubMed:8451767 ]
Chan KL, Sugiyama H, Saito I, Hara M: DNA cleavage reaction of antitumour antibiotic, kapurimycin A3, with deoxytetranucleotide d(CGCG)2. Tetrahedron Lett. 1991;32(52):7719-22. [PubMed:30260325 ]
Sugiyama H, Lam CK, Hosoda M, Saito I: Site specific covalent alkylation of DNA by antitumor antibiotics, duocarmycin A and kapurimycin A3. Nucleic Acids Symp Ser. 1991;(25):75-6. [PubMed:1842103 ]
LOTUS database [Link]

Showing NP-Card for [(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid (NP0326237)

MOL for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

3D MOL for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

3D SDF for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

3D-SDF for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

PDB for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

3D PDB for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

SMILES for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

INCHI for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

Structure for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)

3D Structure for NP0326237 ([(8s)-8-(acetyloxy)-12-hydroxy-2-[(2s,3r)-2-methyl-3-[(1z)-prop-1-en-1-yl]oxiran-2-yl]-4,11-dioxo-9,10-dihydro-8h-1-oxatetraphen-5-yl]acetic acid)