NP-MRD: Showing NP-Card for (2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid (NP0174593)

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Record Information

Version

2.0

Created at

2022-09-03 11:52:33 UTC

Updated at

2022-09-03 11:52:33 UTC

NP-MRD ID

NP0174593

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid

Description

(2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-6H,7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid belongs to the class of organic compounds known as fluorenes. Fluorenes are compounds containing a fluorene moiety, which consists of two benzene rings connected through either a cyclopentane, cyclopentene, or cyclopenta-1,3-diene. Based on a literature review very few articles have been published on (2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-6H,7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032213522D          

 35 38  0  0  1  0            999 V2000
   -1.5907   -1.1456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1782   -1.8601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5907   -2.5746    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1782   -3.2891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5907   -4.0035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1782   -4.7180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3532   -4.7180    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0593   -5.4325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8843   -5.4325    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2968   -6.1469    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8843   -6.8614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8843   -4.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4157   -4.0035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.1301    0.6493    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4627    0.1644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7090    0.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309032213522D          

 35 38  0  0  1  0            999 V2000
   -1.5907   -1.1456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1782   -1.8601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0174593

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H]1CCC(=O)C2=C1C(O)=C1CC3=C(C1=C2O)C(OC)=CC(CSC[C@@H](N=C(C)O)C(O)=O)=C3

> <INCHI_IDENTIFIER>
InChI=1S/C25H27NO8S/c1-11(27)26-15(25(31)32)10-35-9-12-6-13-8-14-20(19(13)18(7-12)34-3)24(30)21-16(28)4-5-17(33-2)22(21)23(14)29/h6-7,15,17,29-30H,4-5,8-10H2,1-3H3,(H,26,27)(H,31,32)/t15-,17-/m1/s1

> <INCHI_KEY>
XSTMCEQPHBSFEK-NVXWUHKLSA-N

> <FORMULA>
C25H27NO8S

> <MOLECULAR_WEIGHT>
501.55

> <EXACT_MASS>
501.145738007

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
53.522832520302366

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-6H,7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid

> <ALOGPS_LOGP>
2.68

> <JCHEM_LOGP>
3.4871617006666664

> <ALOGPS_LOGS>
-4.38

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
5.777062555117417

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.679455889072778

> <JCHEM_PKA_STRONGEST_BASIC>
0.8585733003418495

> <JCHEM_POLAR_SURFACE_AREA>
145.88

> <JCHEM_REFRACTIVITY>
131.27769999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.08e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.969  -2.139   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -2.199  -3.472   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -2.969  -4.806   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.199  -6.140   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.969  -7.473   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.199  -8.807   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      -0.659  -8.807   0.000  0.00  0.00           S+0
HETATM    8  C   UNK     0       0.111 -10.141   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.651 -10.141   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.421 -11.474   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.651 -12.808   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.421 -14.142   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.111 -12.808   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.421  -8.807   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.651  -7.473   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.961  -8.807   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -4.509  -7.473   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.279  -6.140   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.509  -4.806   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.540  -3.661   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.379  -2.130   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -3.972  -1.504   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -6.625  -1.225   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -8.032  -1.851   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.193  -3.383   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -9.599  -4.009   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -6.947  -4.288   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -6.786  -5.819   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -9.277  -0.946   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0     -10.684  -1.572   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0     -10.845  -3.104   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -9.116   0.586   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -7.710   1.212   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -6.464   0.307   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -5.057   0.933   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    9   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    5   18                                                       
CONECT   18   17   19   28                                                  
CONECT   19   18    3   20                                                  
CONECT   20   19   21   27                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   34                                                  
CONECT   24   23   25   29                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   20   28                                                  
CONECT   28   27   18                                                       
CONECT   29   24   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   23   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
(2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-6H,7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoate	Generator
(2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-6H,7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulphanyl)-2-[(1-hydroxyethylidene)amino]propanoate	Generator
(2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-6H,7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulphanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid	Generator

Chemical Formula

C₂₅H₂₇NO₈S

Average Mass

501.5500 Da

Monoisotopic Mass

501.14574 Da

IUPAC Name

(2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-6H,7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid

Traditional Name

(2S)-3-({[(9R)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7H,8H,9H,11H-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid

CAS Registry Number

Not Available

SMILES

CO[C@@H]1CCC(=O)C2=C1C(O)=C1CC3=C(C1=C2O)C(OC)=CC(CSC[C@@H](N=C(C)O)C(O)=O)=C3

InChI Identifier

InChI=1S/C25H27NO8S/c1-11(27)26-15(25(31)32)10-35-9-12-6-13-8-14-20(19(13)18(7-12)34-3)24(30)21-16(28)4-5-17(33-2)22(21)23(14)29/h6-7,15,17,29-30H,4-5,8-10H2,1-3H3,(H,26,27)(H,31,32)/t15-,17-/m1/s1

InChI Key

XSTMCEQPHBSFEK-NVXWUHKLSA-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 fluorenes. Fluorenes are compounds containing a fluorene moiety, which consists of two benzene rings connected through either a cyclopentane, cyclopentene, or cyclopenta-1,3-diene.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Fluorenes

Sub Class

Not Available

Direct Parent

Fluorenes

Alternative Parents

Substituents

N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
Fluorene
Cysteine or derivatives
Tetralin
Alpha-amino acid or derivatives
Aryl alkyl ketone
Aryl ketone
Anisole
Alkyl aryl ether
Vinylogous acid
Ketone
Dialkylthioether
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Sulfenyl compound
Thioether
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic 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	2.68	ALOGPS
logP	3.49	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	3.68	ChemAxon
pKa (Strongest Basic)	0.86	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	145.88 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	131.28 m³·mol⁻¹	ChemAxon
Polarizability	53.52 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

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

162971447

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid (NP0174593)

MOL for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

3D MOL for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

3D SDF for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

3D-SDF for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

PDB for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

3D PDB for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

SMILES for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

INCHI for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

Structure for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)

3D Structure for NP0174593 ((2s)-3-({[(9r)-5,10-dihydroxy-4,9-dimethoxy-6-oxo-7h,8h,9h,11h-cyclohexa[b]fluoren-2-yl]methyl}sulfanyl)-2-[(1-hydroxyethylidene)amino]propanoic acid)