NP-MRD: Showing NP-Card for 6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid (NP0292743)

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Record Information

Version

2.0

Created at

2022-09-10 00:25:16 UTC

Updated at

2022-09-10 00:25:16 UTC

NP-MRD ID

NP0292743

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid

Description

Dethiobiotin belongs to the class of organic compounds known as imidazolyl carboxylic acids and derivatives. These are organic compounds containing a carboxylic acid chain (of at least 2 carbon atoms) linked to an imidazole ring. Dethiobiotin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid is found in Apis cerana and Synechococcus elongatus. 6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid was first documented in 2020 (PMID: 32220614). Based on a literature review a small amount of articles have been published on dethiobiotin (PMID: 34597430) (PMID: 34533923) (PMID: 33972354).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 33  0  0  0  0  0  0  0  0999 V2000
    3.9581   -1.0995   -0.2191 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8291   -0.3232    0.4681 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4049    0.8950    1.0424 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1827    1.9052    0.2926 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5844    3.2359    0.5217 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4480    1.4995   -0.8506 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9128    0.1689   -0.5908 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4637    0.2948   -0.1876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1162   -1.0158    0.2403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5564   -0.9377    0.6465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4726   -0.4569   -0.4294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8803   -0.4328    0.1290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8482    0.0371   -0.8899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4300    0.3449   -2.0300 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2012    0.1519   -0.6370 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9288   -0.6129   -0.0139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9947   -2.1505    0.1164 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8231   -1.1245   -1.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4178   -0.9814    1.2242 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3458    3.5995   -0.0497 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2874    2.0179   -1.7411 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9257   -0.4558   -1.5141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0671    0.7436   -1.0519 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4405    1.0110    0.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4401   -1.3937    1.1212 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0286   -1.7360   -0.5872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8770   -1.9626    0.9296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6907   -0.3129    1.5480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2545    0.5734   -0.7709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4391   -1.1803   -1.2715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1721   -1.4150    0.5560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8654    0.2807    0.9815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5453    0.8321    0.0093 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  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  1  0
 13 15  1  0
 13 14  2  0
  7  2  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  1
  5 20  1  0
  6 21  1  0
  7 22  1  6
  8 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
M  END


  Mrv1652309102202252D          

 15 15  0  0  0  0            999 V2000
    1.6050   -1.6745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9919   -1.1225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1849   -1.2940    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2276   -0.5795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0481   -0.4933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3244    0.0336    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0781   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7926    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2215    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9360   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6505    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3649   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0794    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3649   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0292743

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1N=C(O)NC1CCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18N2O3/c1-7-8(12-10(15)11-7)5-3-2-4-6-9(13)14/h7-8H,2-6H2,1H3,(H,13,14)(H2,11,12,15)

> <INCHI_KEY>
AUTOLBMXDDTRRT-UHFFFAOYSA-N

> <FORMULA>
C10H18N2O3

> <MOLECULAR_WEIGHT>
214.265

> <EXACT_MASS>
214.131742448

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.28995921282921

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-(2-hydroxy-4-methyl-4,5-dihydro-1H-imidazol-5-yl)hexanoic acid

> <JCHEM_LOGP>
0.011210244651867842

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.381243227626711

> <JCHEM_PKA_STRONGEST_ACIDIC>
-2.6237118945353854

> <JCHEM_PKA_STRONGEST_BASIC>
15.000000000421325

> <JCHEM_POLAR_SURFACE_AREA>
81.92

> <JCHEM_REFRACTIVITY>
54.91969999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-(2-hydroxy-5-methyl-4,5-dihydro-3H-imidazol-4-yl)hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       2.996  -3.126   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.851  -2.095   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.345  -2.415   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -0.425  -1.082   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.956  -0.921   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       0.606   0.063   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       2.012  -0.564   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.346   0.206   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.680  -0.564   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.013   0.206   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.347  -0.564   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.681   0.206   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.015  -0.564   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      11.348   0.206   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      10.015  -2.104   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
Desthiobiotin	ChEBI
Desthiobiotin, (cis)-(+-)-isomer	MeSH
Desthiobiotin, (4R-cis)-isomer	MeSH

Chemical Formula

C₁₀H₁₈N₂O₃

Average Mass

214.2650 Da

Monoisotopic Mass

214.13174 Da

IUPAC Name

6-(2-hydroxy-4-methyl-4,5-dihydro-1H-imidazol-5-yl)hexanoic acid

Traditional Name

6-(2-hydroxy-5-methyl-4,5-dihydro-3H-imidazol-4-yl)hexanoic acid

CAS Registry Number

Not Available

SMILES

CC1N=C(O)NC1CCCCCC(O)=O

InChI Identifier

InChI=1S/C10H18N2O3/c1-7-8(12-10(15)11-7)5-3-2-4-6-9(13)14/h7-8H,2-6H2,1H3,(H,13,14)(H2,11,12,15)

InChI Key

AUTOLBMXDDTRRT-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

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633
Synechococcus elongatus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as imidazolyl carboxylic acids and derivatives. These are organic compounds containing a carboxylic acid chain (of at least 2 carbon atoms) linked to an imidazole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azoles

Sub Class

Imidazoles

Direct Parent

Imidazolyl carboxylic acids and derivatives

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

ureas (CHEBI:16691 )
monocarboxylic acid (CHEBI:16691 )
imidazolidinone (CHEBI:16691 )

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	0.011	ChemAxon
pKa (Strongest Acidic)	-2.6	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	6	ChemAxon
Refractivity	54.92 m³·mol⁻¹	ChemAxon
Polarizability	23.29 Å³	ChemAxon
Number of Rings	1	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

Not Available

KNApSAcK ID

C00000757

Chemspider ID

623

KEGG Compound ID

C01909

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

643

PDB ID

Not Available

ChEBI ID

16691

Good Scents ID

Not Available

References

General References

Song X, Cronan JE: A conserved and seemingly redundant Escherichia coli biotin biosynthesis gene expressed only during anaerobic growth. Mol Microbiol. 2021 Nov;116(5):1315-1327. doi: 10.1111/mmi.14826. Epub 2021 Oct 18. [PubMed:34597430 ]
Schumann NC, Lee KJ, Thompson AP, Salaemae W, Pederick JL, Avery T, Gaiser BI, Hodgkinson-Bean J, Booker GW, Polyak SW, Bruning JB, Wegener KL, Abell AD: Inhibition of Mycobacterium tuberculosis Dethiobiotin Synthase (MtDTBS): Toward Next-Generation Antituberculosis Agents. ACS Chem Biol. 2021 Nov 19;16(11):2339-2347. doi: 10.1021/acschembio.1c00491. Epub 2021 Sep 17. [PubMed:34533923 ]
Ren X, Chen Z, Niu P, Han W, Ding C, Yu S: XRE-Type Regulator BioX Acts as a Negative Transcriptional Factor of Biotin Metabolism in Riemerella anatipestifer. J Bacteriol. 2021 Jul 8;203(15):e0018121. doi: 10.1128/JB.00181-21. Epub 2021 Jul 8. [PubMed:33972354 ]
Bali AP, Lennox-Hvenekilde D, Myling-Petersen N, Buerger J, Salomonsen B, Gronenberg LS, Sommer MOA, Genee HJ: Improved biotin, thiamine, and lipoic acid biosynthesis by engineering the global regulator IscR. Metab Eng. 2020 Jul;60:97-109. doi: 10.1016/j.ymben.2020.03.005. Epub 2020 Mar 25. [PubMed:32220614 ]
LOTUS database [Link]

Showing NP-Card for 6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid (NP0292743)

MOL for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

3D MOL for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

3D SDF for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

3D-SDF for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

PDB for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

3D PDB for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

SMILES for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

INCHI for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

Structure for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)

3D Structure for NP0292743 (6-(2-hydroxy-5-methyl-4,5-dihydro-3h-imidazol-4-yl)hexanoic acid)