NP-MRD: Showing NP-Card for 5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid (NP0321058)

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Record Information

Version

2.0

Created at

2022-09-11 23:03:50 UTC

Updated at

2022-09-11 23:03:50 UTC

NP-MRD ID

NP0321058

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid

Description

5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid is found in Apis cerana.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
   -5.1104    0.1976    1.5893 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4089   -0.0235    0.3504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0543    0.0459   -0.7149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9571   -0.3266    0.3311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5217   -0.5034   -1.0818 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0564   -0.8168   -1.2242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1771    0.2757   -0.6557 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2358   -0.1413   -0.8516 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5147   -1.7265    0.0321 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.0904   -1.2830    0.8664 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4982   -0.0706    0.0509 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2026    0.8103    0.9650 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1907    1.4521    1.7318 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4198    2.1186    2.7677 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9115    1.1955    1.1104 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2475    0.7314   -0.2133 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.7571   -0.2871    2.4286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9331    0.8297    1.5816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4439    0.5331    0.7954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7610   -1.2776    0.8758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1038   -1.2956   -1.5916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7040    0.4363   -1.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8097   -1.7520   -0.6484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7492   -1.0031   -2.2535 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4213    0.5063    0.3978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3620    1.1845   -1.2970 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4575   -0.2409   -1.9167 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8756   -1.0024    1.8971 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8152   -2.0940    0.7457 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0657   -0.3221   -0.8403 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2336    0.9097    1.0050 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0125    1.3420    1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5597    1.5978   -0.8289 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  1  1  0
  2  3  2  0
  8 16  1  0
 16 15  1  0
 15 13  1  0
 13 14  2  0
 13 12  1  0
 16 11  1  0
 12 11  1  0
 11 30  1  6
 10 28  1  0
 10 29  1  0
  8 27  1  6
  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
  1 17  1  0
  1 18  1  0
 16 33  1  6
 15 32  1  0
 12 31  1  0
M  END

 
  Mrv1533006081518282D          
 
 18 19  0  0  1  0            999 V2000
   14.3393  -12.7560    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.5100  -12.7598    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.5969  -13.5438    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.5893  -11.9682    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.2561  -11.9758    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.2638  -13.5514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9303  -14.0247    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   15.4227  -13.5475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9151  -11.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1384  -13.9567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9076  -10.8302    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8505  -13.5400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5663  -13.9491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2745  -13.5325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2670  -12.7106    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.9903  -13.9414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.1651  -12.7522    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6881  -12.7598    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  6  0  0  0
  4  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  1 17  1  1  0  0  0
  2 18  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0321058

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H17N3O2S/c11-8(14)4-2-1-3-7-9-6(5-16-7)12-10(15)13-9/h6-7,9H,1-5H2,(H2,11,14)(H2,12,13,15)/t6-,7-,9-/m0/s1

> <INCHI_KEY>
XFLVBMBRLSCJAI-ZKWXMUAHSA-N

> <FORMULA>
C10H17N3O2S

> <MOLECULAR_WEIGHT>
243.33

> <EXACT_MASS>
243.104147973

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.06455703913685

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4-d]imidazolidin-4-yl]pentanamide

> <ALOGPS_LOGP>
-0.20

> <JCHEM_LOGP>
-0.48751896566666636

> <ALOGPS_LOGS>
-2.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.176192228163625

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.600546792148126

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2578591953488352

> <JCHEM_POLAR_SURFACE_AREA>
84.22

> <JCHEM_REFRACTIVITY>
61.87310000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.81e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
biotinamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-JUN-15         0                                  
HETATM    1  C   UNK     0      26.767 -23.811   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      25.219 -23.818   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.248 -25.282   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      27.233 -22.341   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      24.745 -22.355   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      24.759 -25.296   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      26.003 -26.179   0.000  0.00  0.00           S+0
HETATM    8  C   UNK     0      28.789 -25.289   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      25.975 -21.450   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      30.125 -26.052   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      25.961 -20.216   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      31.454 -25.275   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      32.790 -26.038   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      34.112 -25.261   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      34.098 -23.726   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      35.449 -26.024   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0      28.308 -23.804   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0      23.685 -23.818   0.000  0.00  0.00           H+0
CONECT    1    2    3    4   17                                             
CONECT    2    1    5    6   18                                             
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2    9                                                       
CONECT    6    2    7                                                       
CONECT    7    3    6                                                       
CONECT    8    3   10                                                       
CONECT    9    4   11    5                                                  
CONECT   10    8   12                                                       
CONECT   11    9                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    1                                                            
CONECT   18    2                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
Biotinamide	ChEBI

Chemical Formula

C₁₀H₁₇N₃O₂S

Average Mass

243.3300 Da

Monoisotopic Mass

243.10415 Da

IUPAC Name

5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4-d]imidazolidin-4-yl]pentanamide

Traditional Name

biotinamide

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C10H17N3O2S/c11-8(14)4-2-1-3-7-9-6(5-16-7)12-10(15)13-9/h6-7,9H,1-5H2,(H2,11,14)(H2,12,13,15)/t6-,7-,9-/m0/s1

InChI Key

XFLVBMBRLSCJAI-ZKWXMUAHSA-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
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

This compound 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
Thienoimidazolidine
Fatty acyl
Imidazolidinone
Fatty amide
Thiophene
Thiolane
Imidazolidine
Urea
Primary carboxylic acid amide
Carboxamide group
Azacycle
Dialkylthioether
Thioether
Carboxylic acid derivative
Carboxylic acid amide
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid amide (CHEBI:16615 )
biotins (CHEBI:16615 )

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	-0.2	ALOGPS
logP	-0.49	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	13.6	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	84.22 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	61.87 m³·mol⁻¹	ChemAxon
Polarizability	25.06 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

75650

KEGG Compound ID

C01893

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

83831

PDB ID

Not Available

ChEBI ID

16615

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid (NP0321058)

MOL for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

3D MOL for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

3D SDF for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

3D-SDF for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

PDB for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

3D PDB for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

SMILES for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

INCHI for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

Structure for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)

3D Structure for NP0321058 (5-[(3as,4s,6ar)-2-hydroxy-3h,3ah,4h,6h,6ah-thieno[3,4-d]imidazol-4-yl]pentanimidic acid)