NP-MRD: Showing NP-Card for Sirodesmin H (NP0051381)

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Record Information

Version

2.0

Created at

2022-04-27 22:46:12 UTC

Updated at

2022-04-27 22:46:12 UTC

NP-MRD ID

NP0051381

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sirodesmin H

Description

Sirodesmin H is found in Phoma lingam. Based on a literature review very few articles have been published on (1'R,2S,3'S,4'S,5R,7'R,10'S)-3'-hydroxy-10'-(hydroxymethyl)-4,4,5,11'-tetramethyl-3,9',12'-trioxo-13'-thia-8',11'-diazaspiro[oxolane-2,5'-tetracyclo[8.2.1.0¹,⁸.0³,⁷]Tridecane]-4'-yl acetate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200462D          

 31 35  0  0  1  0            999 V2000
    3.5166   -0.1905    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5514    0.6338    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3460    0.8554    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8024    0.1681    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2898   -0.4783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3150    0.8145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0934    1.6092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0882    0.5267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0534   -0.2975    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2588   -0.5192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6998   -0.8102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4630    1.2617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9110    0.5869    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6338    1.6286    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1081    2.2644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2946    2.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3959    3.0376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7522    0.8736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1602    0.2195    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6735   -0.4395    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0969   -1.0474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2375   -1.8604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3103   -0.6483    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9311    0.3616    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6487    0.8589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7679    1.6752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1437    0.6075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2076   -0.0991    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6957   -1.1986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0882   -0.9415    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5594    1.4587    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
  1  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  1  0  0  0
  9 11  1  1  0  0  0
  8 12  1  0  0  0  0
  8 13  1  0  0  0  0
  3 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
  2 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  1 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 19 25  1  0  0  0  0
 25 26  2  0  0  0  0
 24 27  1  0  0  0  0
 23 28  1  0  0  0  0
 19 28  1  1  0  0  0
 23 29  1  6  0  0  0
 29 30  1  0  0  0  0
  2 31  1  6  0  0  0
M  END


  Mrv1652304282200462D          

 31 35  0  0  1  0            999 V2000
    3.5166   -0.1905    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5514    0.6338    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3460    0.8554    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8024    0.1681    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2898   -0.4783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3150    0.8145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0934    1.6092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0882    0.5267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0534   -0.2975    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2588   -0.5192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6998   -0.8102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4630    1.2617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9110    0.5869    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6338    1.6286    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1081    2.2644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2946    2.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3959    3.0376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7522    0.8736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1602    0.2195    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6735   -0.4395    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0969   -1.0474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2375   -1.8604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3103   -0.6483    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9311    0.3616    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6487    0.8589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7679    1.6752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1437    0.6075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2076   -0.0991    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6957   -1.1986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0882   -0.9415    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5594    1.4587    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
  1  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  1  0  0  0
  9 11  1  1  0  0  0
  8 12  1  0  0  0  0
  8 13  1  0  0  0  0
  3 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
  2 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  1 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 19 25  1  0  0  0  0
 25 26  2  0  0  0  0
 24 27  1  0  0  0  0
 23 28  1  0  0  0  0
 19 28  1  1  0  0  0
 23 29  1  6  0  0  0
 29 30  1  0  0  0  0
  2 31  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0051381

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1O[C@]2(C[C@H]3N4C(=O)[C@@]5(CO)S[C@]4(C[C@@]3(O)[C@@H]2OC(C)=O)C(=O)N5C)C(=O)C1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C20H26N2O8S/c1-9-16(3,4)12(25)18(30-9)6-11-17(28,13(18)29-10(2)24)7-19-14(26)21(5)20(8-23,31-19)15(27)22(11)19/h9,11,13,23,28H,6-8H2,1-5H3/t9-,11-,13+,17+,18-,19-,20+/m1/s1

> <INCHI_KEY>
ITMLCHOGYDYPNT-VCMNAWNDSA-N

> <FORMULA>
C20H26N2O8S

> <MOLECULAR_WEIGHT>
454.49

> <EXACT_MASS>
454.140986979

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
57

> <JCHEM_AVERAGE_POLARIZABILITY>
44.63398864018845

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1'R,2S,3'S,4'S,5R,7'R,10'R)-3'-hydroxy-10'-(hydroxymethyl)-4,4,5,11'-tetramethyl-3,9',12'-trioxo-13'-thia-8',11'-diazaspiro[oxolane-2,5'-tetracyclo[8.2.1.0^{1,8}.0^{3,7}]tridecane]-4'-yl acetate

> <ALOGPS_LOGP>
0.36

> <JCHEM_LOGP>
0.1873416093333331

> <ALOGPS_LOGS>
-2.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.181062715478884

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.981221058508222

> <JCHEM_PKA_STRONGEST_BASIC>
-3.170382313231795

> <JCHEM_POLAR_SURFACE_AREA>
133.68

> <JCHEM_REFRACTIVITY>
104.9717

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.50e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1'R,2S,3'S,4'S,5R,7'R,10'R)-3'-hydroxy-10'-(hydroxymethyl)-4,4,5,11'-tetramethyl-3,9',12'-trioxo-13'-thia-8',11'-diazaspiro[oxolane-2,5'-tetracyclo[8.2.1.0^{1,8}.0^{3,7}]tridecane]-4'-yl acetate

> <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       6.564  -0.356   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.629   1.183   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.113   1.597   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.964   0.314   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.008  -0.893   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.921   1.520   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       9.508   3.004   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      11.365   0.983   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.300  -0.555   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       9.816  -0.969   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      12.506  -1.512   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.064   2.355   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.901   1.096   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.650   3.040   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       7.669   4.227   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.150   3.970   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.206   5.670   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.137   1.631   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.032   0.410   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       4.991  -0.820   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       3.914  -1.955   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.177  -3.473   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.446  -1.210   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       1.738   0.675   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       3.078   1.603   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       3.300   3.127   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       0.268   1.134   0.000  0.00  0.00           C+0
HETATM   28  S   UNK     0       2.254  -0.185   0.000  0.00  0.00           S+0
HETATM   29  C   UNK     0       1.299  -2.237   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -0.165  -1.757   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       6.644   2.723   0.000  0.00  0.00           O+0
CONECT    1    2    5   20                                                  
CONECT    2    1    3   18   31                                             
CONECT    3    2    4   14                                                  
CONECT    4    3    5    6   10                                             
CONECT    5    4    1                                                       
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   12   13                                             
CONECT    9    8   10   11                                                  
CONECT   10    9    4                                                       
CONECT   11    9                                                            
CONECT   12    8                                                            
CONECT   13    8                                                            
CONECT   14    3   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18    2   19                                                       
CONECT   19   18   20   25   28                                             
CONECT   20   19    1   21                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   28   29                                             
CONECT   24   23   25   27                                                  
CONECT   25   24   19   26                                                  
CONECT   26   25                                                            
CONECT   27   24                                                            
CONECT   28   23   19                                                       
CONECT   29   23   30                                                       
CONECT   30   29                                                            
CONECT   31    2                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

View in JSmol

Synonyms

Value	Source
(1'r,2S,3's,4's,5R,7'r,10's)-3'-Hydroxy-10'-(hydroxymethyl)-4,4,5,11'-tetramethyl-3,9',12'-trioxo-13'-thia-8',11'-diazaspiro[oxolane-2,5'-tetracyclo[8.2.1.0,.0,]tridecane]-4'-yl acetic acid	Generator

Chemical Formula

C₂₀H₂₆N₂O₈S

Average Mass

454.4900 Da

Monoisotopic Mass

454.14099 Da

IUPAC Name

(1'R,2S,3'S,4'S,5R,7'R,10'R)-3'-hydroxy-10'-(hydroxymethyl)-4,4,5,11'-tetramethyl-3,9',12'-trioxo-13'-thia-8',11'-diazaspiro[oxolane-2,5'-tetracyclo[8.2.1.0^{1,8}.0^{3,7}]tridecane]-4'-yl acetate

Traditional Name

(1'R,2S,3'S,4'S,5R,7'R,10'R)-3'-hydroxy-10'-(hydroxymethyl)-4,4,5,11'-tetramethyl-3,9',12'-trioxo-13'-thia-8',11'-diazaspiro[oxolane-2,5'-tetracyclo[8.2.1.0^{1,8}.0^{3,7}]tridecane]-4'-yl acetate

CAS Registry Number

Not Available

SMILES

C[C@H]1O[C@]2(C[C@H]3N4C(=O)[C@@]5(CO)S[C@]4(C[C@@]3(O)[C@@H]2OC(C)=O)C(=O)N5C)C(=O)C1(C)C

InChI Identifier

InChI=1S/C20H26N2O8S/c1-9-16(3,4)12(25)18(30-9)6-11-17(28,13(18)29-10(2)24)7-19-14(26)21(5)20(8-23,31-19)15(27)22(11)19/h9,11,13,23,28H,6-8H2,1-5H3/t9-,11-,13+,17+,18-,19-,20+/m1/s1

InChI Key

ITMLCHOGYDYPNT-VCMNAWNDSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Leptosphaeria maculans	Fungi	KNApSAcK

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	0.36	ALOGPS
logP	0.19	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	12.98	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	133.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	104.97 m³·mol⁻¹	ChemAxon
Polarizability	44.63 Å³	ChemAxon
Number of Rings	5	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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Sirodesmin H (NP0051381)

MOL for NP0051381 (Sirodesmin H)

3D MOL for NP0051381 (Sirodesmin H)

3D SDF for NP0051381 (Sirodesmin H)

3D-SDF for NP0051381 (Sirodesmin H)

PDB for NP0051381 (Sirodesmin H)

3D PDB for NP0051381 (Sirodesmin H)

SMILES for NP0051381 (Sirodesmin H)

INCHI for NP0051381 (Sirodesmin H)

Structure for NP0051381 (Sirodesmin H)

3D Structure for NP0051381 (Sirodesmin H)