NP-MRD: Showing NP-Card for 5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid (NP0172320)

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Record Information

Version

2.0

Created at

2022-09-03 09:12:20 UTC

Updated at

2022-09-03 09:12:20 UTC

NP-MRD ID

NP0172320

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid

Description

Biotin belongs to the class of organic compounds known as biotin and derivatives. These are organic compounds containing a ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring. Biotin is an extremely strong basic compound (based on its pKa). In humans, biotin is involved in the metabolic disorder called the biotinidase deficiency pathway. Outside of the human body, Biotin is found, on average, in the highest concentration within a few different foods, such as leavening agents, true oysters, and oyster mushrooms and in a lower concentration in pepper (c. Annuum), cauliflowers, and biscuits. Biotin has also been detected, but not quantified in, several different foods, such as sorghums, cowpea, canola, purple mangosteens, and european cranberries. This could make biotin a potential biomarker for the consumption of these foods. The frequency of marginal biotin status is not known, but the incidence of low circulating biotin levels in alcoholics has been found to be much greater than in the general population.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    5.7414   -0.1027    0.0285 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7504    0.6451   -0.0916 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8779    1.8963   -0.6538 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4200    0.1869    0.3749 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7688   -0.7548   -0.5876 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4436   -1.2031   -0.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4548   -0.0876    0.1602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8128   -0.7172    0.6654 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4942   -1.9064   -0.5267 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2577   -1.5064   -0.2837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2348   -0.5037    0.8488 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1771    0.5418    0.4360 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5411    1.4233   -0.2795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1454    2.5666   -0.8410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1705    1.0466   -0.3943 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9438    0.2379    0.7935 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4917    2.1380   -1.5448 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7708    1.0900    0.5208 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4982   -0.2924    1.3628 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5965   -0.2696   -1.5943 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4094   -1.6355   -0.8229 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0490   -1.9585   -0.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5884   -1.7998    0.8874 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2932    0.4042   -0.8196 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8802    0.6401    0.8443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6687   -1.2347    1.6111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7669   -2.4530   -0.0235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6025   -1.0623   -1.2420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4832   -0.9311    1.8194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3114    3.4043   -0.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5439    1.3235   -1.1736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8805    0.8741    1.6979 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16  8  1  0
 16 11  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  1
 10 27  1  0
 10 28  1  0
 11 29  1  1
 14 30  1  0
 15 31  1  0
 16 32  1  1
M  END


  Mrv1652305221920272D          

 16 17  0  0  0  0            999 V2000
    4.7579   -3.7632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0434   -4.1757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4724   -4.1757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3289   -3.7632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0800   -2.7712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4925   -3.4856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1868   -3.7632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6145   -4.1757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9405   -4.0987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1600   -4.6417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2462   -3.8212    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.3530   -4.8132    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9000   -3.7632    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6145   -5.0007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7731   -5.1937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2731   -2.9427    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  1  0  0  0  0
 11  6  1  0  0  0  0
 11 10  2  0  0  0  0
 12  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  8  2  0  0  0  0
 14  8  1  0  0  0  0
 15 10  1  0  0  0  0
 16  5  1  0  0  0  0
 16  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0172320

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CCCCC1SCC2N=C(O)NC12

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)

> <INCHI_KEY>
YBJHBAHKTGYVGT-UHFFFAOYSA-N

> <FORMULA>
C10H16N2O3S

> <MOLECULAR_WEIGHT>
244.311

> <EXACT_MASS>
244.088163078

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.349124816648512

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-{2-hydroxy-1H,3aH,4H,6H,6aH-thieno[3,4-d]imidazol-6-yl}pentanoic acid

> <ALOGPS_LOGP>
0.30

> <JCHEM_LOGP>
-0.3949622777343877

> <ALOGPS_LOGS>
-2.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.143063323689655

> <JCHEM_PKA_STRONGEST_ACIDIC>
-3.4349619501272306

> <JCHEM_PKA_STRONGEST_BASIC>
15.000000000260885

> <JCHEM_POLAR_SURFACE_AREA>
81.92

> <JCHEM_REFRACTIVITY>
60.5726

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.34e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-{2-hydroxy-3H,3aH,4H,6H,6aH-thieno[3,4-d]imidazol-4-yl}pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       8.881  -7.025   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.548  -7.795   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.215  -7.795   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.214  -7.025   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.216  -5.173   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.986  -6.507   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.549  -7.025   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.880  -7.795   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.956  -7.651   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      15.232  -8.664   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      15.393  -7.133   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      13.726  -8.985   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       3.547  -7.025   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.880  -9.335   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      16.376  -9.695   0.000  0.00  0.00           O+0
HETATM   16  S   UNK     0      11.710  -5.493   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    6   16                                                       
CONECT    6    5    9   11                                                  
CONECT    7    3    9   16                                                  
CONECT    8    4   13   14                                                  
CONECT    9    6    7   12                                                  
CONECT   10   11   12   15                                                  
CONECT   11    6   10                                                       
CONECT   12    9   10                                                       
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15   10                                                            
CONECT   16    5    7                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₆N₂O₃S

Average Mass

244.3110 Da

Monoisotopic Mass

244.08816 Da

IUPAC Name

5-{2-hydroxy-1H,3aH,4H,6H,6aH-thieno[3,4-d]imidazol-6-yl}pentanoic acid

Traditional Name

5-{2-hydroxy-3H,3aH,4H,6H,6aH-thieno[3,4-d]imidazol-4-yl}pentanoic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CCCCC1SCC2N=C(O)NC12

InChI Identifier

InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)

InChI Key

YBJHBAHKTGYVGT-UHFFFAOYSA-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 biotin and derivatives. These are organic compounds containing a ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Biotin and derivatives

Sub Class

Not Available

Direct Parent

Biotin and derivatives

Alternative Parents

Substituents

Biotin
Imidazolyl carboxylic acid derivative
Medium-chain fatty acid
Heterocyclic fatty acid
Thia fatty acid
Fatty acid
Fatty acyl
Thiolane
2-imidazoline
Isourea
Azacycle
Dialkylthioether
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Carboxylic acid derivative
Thioether
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organonitrogen compound
Organopnictogen compound
Organooxygen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	0.3	ALOGPS
logP	-0.39	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	-3.4	ChemAxon
pKa (Strongest Basic)	15	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	81.92 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	60.57 m³·mol⁻¹	ChemAxon
Polarizability	25.35 Å³	ChemAxon
Number of Rings	2	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

FDB014510

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Biotin

METLIN ID

Not Available

PubChem Compound

253

PDB ID

Not Available

ChEBI ID

95156

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid (NP0172320)

MOL for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

3D MOL for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

3D SDF for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

3D-SDF for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

PDB for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

3D PDB for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

SMILES for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

INCHI for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

Structure for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)

3D Structure for NP0172320 (5-{2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl}pentanoic acid)