NP-MRD: Showing NP-Card for (9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one (NP0221051)

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Record Information

Version

2.0

Created at

2022-09-05 22:31:48 UTC

Updated at

2022-09-05 22:31:48 UTC

NP-MRD ID

NP0221051

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one

Description

(9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one was first documented in 2008 (PMID: 18368162). Based on a literature review a significant number of articles have been published on spiruchostatin B (PMID: 25078973) (PMID: 22684370) (PMID: 27108737) (PMID: 22211246) (PMID: 21445425) (PMID: 19760730).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062200312D          

 32 33  0  0  1  0            999 V2000
   -0.3602    1.3961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3949    0.5718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3016    0.1296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2669   -0.6947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0328    0.5117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8994    1.3508    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7257    1.3381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3080    1.9226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7420    0.4859    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5914    0.6972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3259    1.1577    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.1435    0.9686    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.6537    0.2767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0548   -0.4859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0187   -1.3407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309062200312D          

 32 33  0  0  1  0            999 V2000
   -0.3602    1.3961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0221051

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)C1N=C(O)[C@H]2CSSCC\C=C/C(CC(O)=N[C@H](C)C(O)=N2)OC(=O)CC1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H33N3O6S2/c1-4-12(2)19-16(25)10-18(27)30-14-7-5-6-8-31-32-11-15(21(29)24-19)23-20(28)13(3)22-17(26)9-14/h5,7,12-16,19,25H,4,6,8-11H2,1-3H3,(H,22,26)(H,23,28)(H,24,29)/b7-5-/t12?,13-,14?,15-,16?,19?/m1/s1

> <INCHI_KEY>
MJHZJODQLYCXHE-JITRVDHBSA-N

> <FORMULA>
C21H33N3O6S2

> <MOLECULAR_WEIGHT>
487.63

> <EXACT_MASS>
487.181078143

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
49.127238586366545

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(9S,15E,20R)-6-(butan-2-yl)-5,8,18,21-tetrahydroxy-20-methyl-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one

> <JCHEM_LOGP>
-5.1923893855608485

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
-6.597572446467603

> <JCHEM_PKA_STRONGEST_ACIDIC>
-9.85121294010467

> <JCHEM_PKA_STRONGEST_BASIC>
15.728136220876781

> <JCHEM_POLAR_SURFACE_AREA>
144.3

> <JCHEM_REFRACTIVITY>
126.45299999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(9S,15E,20R)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.672   2.606   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.737   1.067   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.563   0.242   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.498  -1.297   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.928   0.955   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.679   2.521   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       3.221   2.498   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.308   3.589   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.252   0.907   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.837   1.302   0.000  0.00  0.00           C+0
HETATM   11  S   UNK     0       6.208   2.161   0.000  0.00  0.00           S+0
HETATM   12  S   UNK     0       7.734   1.808   0.000  0.00  0.00           S+0
HETATM   13  C   UNK     0       8.687   0.517   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.436  -0.907   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.368  -2.503   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.580  -3.877   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.337  -4.904   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.904  -5.696   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.304  -5.884   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       3.980  -7.389   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       2.931  -5.059   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       2.054  -3.697   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.596  -4.194   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.916  -2.092   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.376  -2.113   0.000  0.00  0.00           O+0
HETATM   26  N   UNK     0       2.013  -0.466   0.000  0.00  0.00           N+0
HETATM   27  O   UNK     0       6.527  -3.552   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.458  -2.427   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       4.309  -3.452   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.462  -1.235   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.193  -0.260   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       2.189  -1.428   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   31                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   26                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   27                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24    9                                                       
CONECT   27   17   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30    5   32                                                  
CONECT   32   31                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

View in JSmol

Synonyms

Value	Source
(1S,7E,9S,13S,14R,19R)-14-Sec-butyl-13-hydroxy-19-methyl-3,4-dithia-15,17,20-triazabicyclo(7.7.6)docos-7-ene-11,16,18,21-tetrone	MeSH

Chemical Formula

C₂₁H₃₃N₃O₆S₂

Average Mass

487.6300 Da

Monoisotopic Mass

487.18108 Da

IUPAC Name

(9S,15E,20R)-6-(butan-2-yl)-5,8,18,21-tetrahydroxy-20-methyl-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one

Traditional Name

(9S,15E,20R)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one

CAS Registry Number

Not Available

SMILES

CCC(C)C1N=C(O)[C@H]2CSSCC\C=C/C(CC(O)=N[C@H](C)C(O)=N2)OC(=O)CC1O

InChI Identifier

InChI=1S/C21H33N3O6S2/c1-4-12(2)19-16(25)10-18(27)30-14-7-5-6-8-31-32-11-15(21(29)24-19)23-20(28)13(3)22-17(26)9-14/h5,7,12-16,19,25H,4,6,8-11H2,1-3H3,(H,22,26)(H,23,28)(H,24,29)/b7-5-/t12?,13-,14?,15-,16?,19?/m1/s1

InChI Key

MJHZJODQLYCXHE-JITRVDHBSA-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

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	-5.2	ChemAxon
pKa (Strongest Acidic)	-9.9	ChemAxon
pKa (Strongest Basic)	15.73	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	144.3 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	126.45 m³·mol⁻¹	ChemAxon
Polarizability	49.13 Å³	ChemAxon
Number of Rings	2	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

101086062

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Rehman MU, Jawaid P, Yoshihisa Y, Li P, Zhao QL, Narita K, Katoh T, Kondo T, Shimizu T: Spiruchostatin A and B, novel histone deacetylase inhibitors, induce apoptosis through reactive oxygen species-mitochondria pathway in human lymphoma U937 cells. Chem Biol Interact. 2014 Sep 25;221:24-34. doi: 10.1016/j.cbi.2014.07.004. Epub 2014 Jul 29. [PubMed:25078973 ]
Kanno S, Maeda N, Tomizawa A, Yomogida S, Katoh T, Ishikawa M: Characterization of cells resistant to the potent histone deacetylase inhibitor spiruchostatin B (SP-B) and effect of overexpressed p21waf1/cip1 on the SP-B resistance or susceptibility of human leukemia cells. Int J Oncol. 2012 Sep;41(3):862-8. doi: 10.3892/ijo.2012.1507. Epub 2012 Jun 6. [PubMed:22684370 ]
Rehman MU, Jawaid P, Zhao QL, Li P, Narita K, Katoh T, Shimizu T, Kondo T: Low-dose spiruchostatin-B, a potent histone deacetylase inhibitor enhances radiation-induced apoptosis in human lymphoma U937 cells via modulation of redox signaling. Free Radic Res. 2016 Jun;50(6):596-610. doi: 10.3109/10715762.2015.1115029. Epub 2016 Apr 24. [PubMed:27108737 ]
Kanno S, Maeda N, Tomizawa A, Yomogida S, Katoh T, Ishikawa M: Involvement of p21waf1/cip1 expression in the cytotoxicity of the potent histone deacetylase inhibitor spiruchostatin B towards susceptible NALM-6 human B cell leukemia cells. Int J Oncol. 2012 May;40(5):1391-6. doi: 10.3892/ijo.2011.1323. Epub 2011 Dec 30. [PubMed:22211246 ]
Fuse S, Okada K, Iijima Y, Munakata A, Machida K, Takahashi T, Takagi M, Shin-ya K, Doi T: Total synthesis of spiruchostatin B aided by an automated synthesizer. Org Biomol Chem. 2011 May 21;9(10):3825-33. doi: 10.1039/c0ob01169j. Epub 2011 Mar 29. [PubMed:21445425 ]
Narita K, Kikuchi T, Watanabe K, Takizawa T, Oguchi T, Kudo K, Matsuhara K, Abe H, Yamori T, Yoshida M, Katoh T: Total synthesis of the bicyclic depsipeptide HDAC inhibitors spiruchostatins A and B, 5''-epi-spiruchostatin B, FK228 (FR901228) and preliminary evaluation of their biological activity. Chemistry. 2009 Oct 26;15(42):11174-86. doi: 10.1002/chem.200901552. [PubMed:19760730 ]
Takizawa T, Watanabe K, Narita K, Oguchi T, Abe H, Katoh T: Total synthesis of spiruchostatin B, a potent histone deacetylase inhibitor, from a microorganism. Chem Commun (Camb). 2008 Apr 14;(14):1677-9. doi: 10.1039/b718310k. Epub 2008 Feb 5. [PubMed:18368162 ]
LOTUS database [Link]

Showing NP-Card for (9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one (NP0221051)

MOL for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

3D MOL for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

3D SDF for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

3D-SDF for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

PDB for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

3D PDB for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

SMILES for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

INCHI for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

Structure for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)

3D Structure for NP0221051 ((9s,15e,20r)-5,8,18,21-tetrahydroxy-20-methyl-6-(sec-butyl)-2-oxa-11,12-dithia-7,19,22-triazabicyclo[7.7.6]docosa-7,15,18,21-tetraen-3-one)