NP-MRD: Showing NP-Card for Geodiamolide K (NP0082643)

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Record Information

Version

2.0

Created at

2022-04-29 03:43:28 UTC

Updated at

2022-04-29 03:43:28 UTC

NP-MRD ID

NP0082643

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Geodiamolide K

Description

(3S,6R,9R,12S,16S,18R)-6-[(3-chloro-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,9,12,16,18-hexamethyl-14-methylidene-1-oxa-4,7,10-triazacyclooctadeca-4,10-diene-2,8,15-trione belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. Geodiamolide K is found in Cymbastela sp. Based on a literature review very few articles have been published on (3S,6R,9R,12S,16S,18R)-6-[(3-chloro-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,9,12,16,18-hexamethyl-14-methylidene-1-oxa-4,7,10-triazacyclooctadeca-4,10-diene-2,8,15-trione.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292205432D          

 39 40  0  0  1  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 12 37  1  6  0  0  0
  8 38  1  6  0  0  0
  2 39  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292205432D          

 39 40  0  0  1  0            999 V2000
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    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  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
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  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
  1 24  1  0  0  0  0
 24 25  1  6  0  0  0
 20 26  1  1  0  0  0
 16 27  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 28 33  1  0  0  0  0
 32 34  1  0  0  0  0
 31 35  1  0  0  0  0
 15 36  1  0  0  0  0
 12 37  1  6  0  0  0
  8 38  1  6  0  0  0
  2 39  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0082643

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@H](C)C(=O)C(=C)C[C@H](C)C(=O)N[C@H](C)C(=O)N(C)[C@H](CC2=CC=C(O)C(Cl)=C2)C(=O)N[C@@H](C)C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C28H38ClN3O7/c1-14-10-16(3)25(35)30-18(5)27(37)32(7)22(13-20-8-9-23(33)21(29)12-20)26(36)31-19(6)28(38)39-17(4)11-15(2)24(14)34/h8-9,12,15-19,22,33H,1,10-11,13H2,2-7H3,(H,30,35)(H,31,36)/t15-,16-,17+,18+,19-,22+/m0/s1

> <INCHI_KEY>
KQYPATLROLRBPQ-MPINGQCISA-N

> <FORMULA>
C28H38ClN3O7

> <MOLECULAR_WEIGHT>
564.08

> <EXACT_MASS>
563.2398283

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
57.88877891895265

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6R,9R,12S,16S,18R)-6-[(3-chloro-4-hydroxyphenyl)methyl]-3,7,9,12,16,18-hexamethyl-14-methylidene-1-oxa-4,7,10-triazacyclooctadecane-2,5,8,11,15-pentone

> <ALOGPS_LOGP>
2.93

> <JCHEM_LOGP>
3.2733882669999987

> <ALOGPS_LOGS>
-4.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.940655543628077

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.938454203213196

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2897193419748492

> <JCHEM_POLAR_SURFACE_AREA>
142.11

> <JCHEM_REFRACTIVITY>
145.49280000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.59e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6R,9R,12S,16S,18R)-6-[(3-chloro-4-hydroxyphenyl)methyl]-3,7,9,12,16,18-hexamethyl-14-methylidene-1-oxa-4,7,10-triazacyclooctadecane-2,5,8,11,15-pentone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       6.668   2.310   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       9.336  -0.770   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0       6.668  -2.310   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   34 Cl   UNK     0       8.002  -7.700   0.000  0.00  0.00          Cl+0
HETATM   35  O   UNK     0      10.669  -9.240   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2   24                                                       
CONECT    2    1    3   39                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   38                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   37                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   36                                                  
CONECT   16   15   17   27                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   26                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23    1   25                                                  
CONECT   25   24                                                            
CONECT   26   20                                                            
CONECT   27   16   28                                                       
CONECT   28   27   29   33                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   35                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32   28                                                       
CONECT   34   32                                                            
CONECT   35   31                                                            
CONECT   36   15                                                            
CONECT   37   12                                                            
CONECT   38    8                                                            
CONECT   39    2                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₈ClN₃O₇

Average Mass

564.0800 Da

Monoisotopic Mass

563.23983 Da

IUPAC Name

(3S,6R,9R,12S,16S,18R)-6-[(3-chloro-4-hydroxyphenyl)methyl]-3,7,9,12,16,18-hexamethyl-14-methylidene-1-oxa-4,7,10-triazacyclooctadecane-2,5,8,11,15-pentone

Traditional Name

(3S,6R,9R,12S,16S,18R)-6-[(3-chloro-4-hydroxyphenyl)methyl]-3,7,9,12,16,18-hexamethyl-14-methylidene-1-oxa-4,7,10-triazacyclooctadecane-2,5,8,11,15-pentone

CAS Registry Number

Not Available

SMILES

C[C@@H]1C[C@H](C)C(=O)C(=C)C[C@H](C)C(=O)N[C@H](C)C(=O)N(C)[C@H](CC2=CC=C(O)C(Cl)=C2)C(=O)N[C@@H](C)C(=O)O1

InChI Identifier

InChI=1S/C28H38ClN3O7/c1-14-10-16(3)25(35)30-18(5)27(37)32(7)22(13-20-8-9-23(33)21(29)12-20)26(36)31-19(6)28(38)39-17(4)11-15(2)24(14)34/h8-9,12,15-19,22,33H,1,10-11,13H2,2-7H3,(H,30,35)(H,31,36)/t15-,16-,17+,18+,19-,22+/m0/s1

InChI Key

KQYPATLROLRBPQ-MPINGQCISA-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
Cymbastela sp.	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Cyclic depsipeptides

Alternative Parents

Substituents

Cyclic depsipeptide
Macrolide
Macrolactam
Alpha-amino acid ester
Alpha-amino acid or derivatives
2-chlorophenol
2-halophenol
1-hydroxy-2-unsubstituted benzenoid
Phenol
Halobenzene
Chlorobenzene
Benzenoid
Monocyclic benzene moiety
Aryl halide
Aryl chloride
Cyclic carboximidic acid
Tertiary carboxylic acid amide
Cyclic ketone
Lactone
Lactam
Ketone
Carboxylic acid ester
Carboxamide group
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	2.93	ALOGPS
logP	3.27	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	7.94	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	142.11 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	145.49 m³·mol⁻¹	ChemAxon
Polarizability	57.89 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

162913067

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Geodiamolide K (NP0082643)

MOL for NP0082643 (Geodiamolide K)

3D MOL for NP0082643 (Geodiamolide K)

3D SDF for NP0082643 (Geodiamolide K)

3D-SDF for NP0082643 (Geodiamolide K)

PDB for NP0082643 (Geodiamolide K)

3D PDB for NP0082643 (Geodiamolide K)

SMILES for NP0082643 (Geodiamolide K)

INCHI for NP0082643 (Geodiamolide K)

Structure for NP0082643 (Geodiamolide K)

3D Structure for NP0082643 (Geodiamolide K)