NP-MRD: Showing NP-Card for (2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol (NP0249259)

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Record Information

Version

2.0

Created at

2022-09-07 11:45:45 UTC

Updated at

2022-09-07 11:45:45 UTC

NP-MRD ID

NP0249259

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol

Description

ZINC13386439 belongs to the class of organic compounds known as 2,5-disubstituted thiophenes. These are organic compounds containing a thiophene that is disubstituted at the C-2, and C5-positions. (2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol is found in Rhaponticum repens, Eclipta alba, Pterocaulon rugosum and Pterocaulon virgatum. Based on a literature review very few articles have been published on ZINC13386439.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072213452D          

 16 16  0  0  1  0            999 V2000
    0.5678    5.2393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    4.4143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    2.7643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8146   -1.4901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2995   -2.1576    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9640   -2.9112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1200   -2.0713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6049   -2.7388    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  3  0  0  0  0
  3  4  1  0  0  0  0
  4  5  3  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  3  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
  9 16  1  0  0  0  0
  6 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0249259

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC#CC#CC1=CC=C(S1)C#C[C@H](O)CCl

> <INCHI_IDENTIFIER>
InChI=1S/C13H9ClOS/c1-2-3-4-5-12-8-9-13(16-12)7-6-11(15)10-14/h8-9,11,15H,10H2,1H3/t11-/m0/s1

> <INCHI_KEY>
YSYBCKHAFOAQDX-NSHDSACASA-N

> <FORMULA>
C13H9ClOS

> <MOLECULAR_WEIGHT>
248.72

> <EXACT_MASS>
248.0062638

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
27.368048297149826

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol

> <JCHEM_LOGP>
3.910427129

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.550405302707397

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8702527205957837

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
63.4298

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       1.060   9.780   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   8.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   6.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   5.160   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.521  -2.782   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.426  -4.027   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.799  -5.434   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -3.957  -3.866   0.000  0.00  0.00           C+0
HETATM   15 Cl   UNK     0      -4.863  -5.112   0.000  0.00  0.00          Cl+0
HETATM   16  S   UNK     0      -0.186   1.175   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   16                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   16                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14                                                            
CONECT   16    9    6                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₉ClOS

Average Mass

248.7200 Da

Monoisotopic Mass

248.00626 Da

IUPAC Name

(2S)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol

Traditional Name

(2S)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol

CAS Registry Number

Not Available

SMILES

CC#CC#CC1=CC=C(S1)C#C[C@H](O)CCl

InChI Identifier

InChI=1S/C13H9ClOS/c1-2-3-4-5-12-8-9-13(16-12)7-6-11(15)10-14/h8-9,11,15H,10H2,1H3/t11-/m0/s1

InChI Key

YSYBCKHAFOAQDX-NSHDSACASA-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

Species Name	Source	Reference
Acroptilon repens	LOTUS Database	35616633
Eclipta alba	LOTUS Database	35616633
Pterocaulon rugosum	LOTUS Database	35616633
Pterocaulon virgatum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2,5-disubstituted thiophenes. These are organic compounds containing a thiophene that is disubstituted at the C-2, and C5-positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Thiophenes

Sub Class

2,5-disubstituted thiophenes

Direct Parent

2,5-disubstituted thiophenes

Alternative Parents

Substituents

2,5-disubstituted thiophene
Heteroaromatic compound
Secondary alcohol
Halohydrin
Chlorohydrin
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organochloride
Organohalogen compound
Alkyl halide
Alkyl chloride
Alcohol
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	3.91	ChemAxon
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	63.43 m³·mol⁻¹	ChemAxon
Polarizability	27.37 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

32788365

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

86310851

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol (NP0249259)

MOL for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

3D MOL for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

3D SDF for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

3D-SDF for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

PDB for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

3D PDB for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

SMILES for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

INCHI for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

Structure for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)

3D Structure for NP0249259 ((2s)-1-chloro-4-[5-(penta-1,3-diyn-1-yl)thiophen-2-yl]but-3-yn-2-ol)