NP-MRD: Showing NP-Card for (3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate (NP0150870)

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Record Information

Version

2.0

Created at

2022-09-02 07:06:05 UTC

Updated at

2022-09-02 07:06:05 UTC

NP-MRD ID

NP0150870

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate

Description

(3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate is found in Trypanosoma brucei.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
    5.0683    1.3256    0.1045 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8077    0.0999    0.1565 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8814   -0.7583    0.3889 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4179   -0.4545   -0.0184 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5289    0.7161   -0.2458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0697    0.3806   -0.4559 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5187   -0.3111    0.7145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8651   -0.7319    0.7423 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9275    0.3089    0.6652 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1678    0.8838   -0.6303 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5412    1.3297   -0.5198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1441    2.4121   -1.1687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1632    0.5511    0.3011 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2477   -0.4653    0.7909 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2320   -1.5471   -0.2634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4455   -1.8729   -0.4822 S   0  0  0  0  0  4  0  0  0  0  0  0
   -1.1085   -1.5340   -1.8931 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7013   -0.4604    0.8742 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1835   -1.0880    0.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4907   -1.1230   -0.9107 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6112    1.3734    0.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9478    1.2810   -1.1188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0476   -0.3034   -1.3519 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5960    1.3514   -0.7051 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1843   -1.2006    0.9318 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6906    0.3486    1.6183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0423   -1.2510    1.7399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9183    1.0354    1.4789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6219    1.0123   -1.4876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4733    3.2353   -0.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4468   -0.8065    1.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6963   -2.4905    0.0865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7042   -1.2468   -1.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 15  1  0
 16 15  1  6
 16 17  2  0
 16  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
  9 14  1  0
 13 14  1  0
 14 31  1  1
 15 32  1  0
 15 33  1  0
  8 27  1  1
  7 25  1  0
  7 26  1  0
  6 23  1  0
  6 24  1  0
  5 21  1  0
  5 22  1  0
  4 19  1  0
  4 20  1  0
  3 18  1  0
  9 28  1  1
 10 29  1  0
 12 30  1  0
M  END


  Mrv0541 08131209382D          

 20 21  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  1  0  0  0  0  0  0  0  0  0
    6.1868   -3.7632    0.0000 C   0  0  1  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  1  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
    5.6600   -2.3907    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
    8.0446   -2.8725    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5092   -4.5226    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6314   -4.8637    0.0000 H   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  6  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
 17  5  1  0  0  0  0
 17  7  1  0  0  0  0
 17 16  2  0  0  0  0
  6 18  1  1  0  0  0
  7 19  1  1  0  0  0
  9 20  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0150870

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12CS(=O)[C@@]([H])(CCCCC(O)=O)[C@@]1([H])NC(O)=N2

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N2O4S/c13-8(14)4-2-1-3-7-9-6(5-17(7)16)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-,17?/m0/s1

> <INCHI_KEY>
KCSKCIQYNAOBNQ-YBSFLMRUSA-N

> <FORMULA>
C10H16N2O4S

> <MOLECULAR_WEIGHT>
260.31

> <EXACT_MASS>
260.0830777

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
25.406391678847616

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(3aR,6S,6aS)-2-hydroxy-5-oxo-1H,3aH,4H,6H,6aH-5λ⁴-thieno[3,4-d]imidazol-6-yl]pentanoic acid

> <ALOGPS_LOGP>
-0.94

> <JCHEM_LOGP>
-2.015660034810551

> <ALOGPS_LOGS>
-1.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.730582913845565

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.581544965786889

> <JCHEM_PKA_STRONGEST_BASIC>
6.066921968708759

> <JCHEM_POLAR_SURFACE_AREA>
98.99000000000001

> <JCHEM_REFRACTIVITY>
62.109899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.41e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(3aS,4S,6aR)-2-hydroxy-5-oxo-3H,3aH,4H,6H,6aH-5λ⁴-thieno[3,4-d]imidazol-4-yl]pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   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   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   18  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    6   17                                                       
CONECT    6    5    9   11   18                                             
CONECT    7    3    9   17   19                                             
CONECT    8    4   13   14                                                  
CONECT    9    6    7   12   20                                             
CONECT   10   11   12   15                                                  
CONECT   11    6   10                                                       
CONECT   12    9   10                                                       
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15   10                                                            
CONECT   16   17                                                            
CONECT   17    5    7   16                                                  
CONECT   18    6                                                            
CONECT   19    7                                                            
CONECT   20    9                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Value	Source
Biotin S-oxide	ChEBI
D-Biotin D-sulphoxide	Generator
D-Biotin-D-sulfoxide	MeSH

Chemical Formula

C₁₀H₁₆N₂O₄S

Average Mass

260.3100 Da

Monoisotopic Mass

260.08308 Da

IUPAC Name

5-[(3aR,6S,6aS)-2-hydroxy-5-oxo-1H,3aH,4H,6H,6aH-5λ⁴-thieno[3,4-d]imidazol-6-yl]pentanoic acid

Traditional Name

5-[(3aS,4S,6aR)-2-hydroxy-5-oxo-3H,3aH,4H,6H,6aH-5λ⁴-thieno[3,4-d]imidazol-4-yl]pentanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@]12CS(=O)[C@@]([H])(CCCCC(O)=O)[C@@]1([H])NC(O)=N2

InChI Identifier

InChI=1S/C10H16N2O4S/c13-8(14)4-2-1-3-7-9-6(5-17(7)16)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-,17?/m0/s1

InChI Key

KCSKCIQYNAOBNQ-YBSFLMRUSA-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
Trypanosoma brucei	LOTUS Database	35616633

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_derivative
Biotin
Thienoimidazolidine
Medium-chain fatty acid
Heterocyclic fatty acid
Imidazolidinone
Fatty acid
Fatty acyl
Imidazolidine
Thiolane
Thiophene
Carbonic acid derivative
Sulfoxide
Urea
Azacycle
Monocarboxylic acid or derivatives
Sulfinyl compound
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

sulfoxide (CHEBI:62193 )
biotins (CHEBI:62193 )

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	-0.94	ALOGPS
logP	-2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	3.58	ChemAxon
pKa (Strongest Basic)	6.07	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	98.99 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	62.11 m³·mol⁻¹	ChemAxon
Polarizability	25.41 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

C20386

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

83833

PDB ID

Not Available

ChEBI ID

62193

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate (NP0150870)

MOL for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

3D MOL for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

3D SDF for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

3D-SDF for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

PDB for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

3D PDB for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

SMILES for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

INCHI for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

Structure for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)

3D Structure for NP0150870 ((3as,4s,6ar)-4-(4-carboxybutyl)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-5-ium-5-olate)