NP-MRD: Showing NP-Card for Djenkolic acid (NP0050677)

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Record Information

Version

2.0

Created at

2022-04-27 22:01:41 UTC

Updated at

2022-04-27 22:01:42 UTC

NP-MRD ID

NP0050677

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Djenkolic acid

Description

L-djenkolic acid, also known as djenkolate, belongs to the class of organic compounds known as l-cysteine-s-conjugates. L-cysteine-S-conjugates are compounds containing L-cysteine where the thio-group is conjugated. L-djenkolic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Djenkolic acid is found in Acacia spp. , Albizia lophantha, Archidendron bubalinum, Mimosa spp., Pithecollobium bubalinum and Pithecolobium lobatum. Djenkolic acid was first documented in 1950 (PMID: 15435518). Based on a literature review a small amount of articles have been published on L-djenkolic acid (PMID: 22212096) (PMID: 22138345) (PMID: 15262924) (PMID: 10555201).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200012D          

 15 14  0  0  1  0            999 V2000
    9.9513    3.2704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.9513    4.0954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2368    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5224    3.2704    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    7.8079    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0934    3.2704    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.3789    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6645    3.2704    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6645    4.0954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.0329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3802    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.0329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  1 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050677

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](CSCSC[C@H](N)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H14N2O4S2/c8-4(6(10)11)1-14-3-15-2-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1

> <INCHI_KEY>
JMQMNWIBUCGUDO-WHFBIAKZSA-N

> <FORMULA>
C7H14N2O4S2

> <MOLECULAR_WEIGHT>
254.32

> <EXACT_MASS>
254.039499287

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
25.62704160517842

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-[({[(2R)-2-amino-2-carboxyethyl]sulfanyl}methyl)sulfanyl]propanoic acid

> <ALOGPS_LOGP>
-3.81

> <JCHEM_LOGP>
-5.440650653830719

> <ALOGPS_LOGS>
-1.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.451310795312687

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6700230934918583

> <JCHEM_PKA_STRONGEST_BASIC>
9.430170568406892

> <JCHEM_POLAR_SURFACE_AREA>
126.64

> <JCHEM_REFRACTIVITY>
58.97330000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.81e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
djenkolic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      18.576   6.105   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      18.576   7.645   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      17.242   5.335   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0      15.908   6.105   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0      14.575   5.335   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0      13.241   6.105   0.000  0.00  0.00           S+0
HETATM    7  C   UNK     0      11.907   5.335   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.574   6.105   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      10.574   7.645   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       9.240   5.335   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       7.906   6.105   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       9.240   3.795   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      19.909   5.335   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      21.243   6.105   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      19.909   3.795   0.000  0.00  0.00           O+0
CONECT    1    2    3   13                                                  
CONECT    2    1                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    1   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

View in JSmol

Synonyms

Value	Source
3,3'-(Methylenedithio)dialanine	ChEBI
3,3'-Methylenedithiobis(2-aminopropanoic acid)	ChEBI
beta,Beta'-methylenedithiodialanine	ChEBI
Djenkolic acid	ChEBI
L-Cysteine thioacetal OF formaldehyde	ChEBI
S,S'-methylene-bis-L-cysteine	ChEBI
S,S'-methylenebis(cysteine)	ChEBI
3,3'-Methylenedithiobis(2-aminopropanoate)	Generator
b,Beta'-methylenedithiodialanine	Generator
Β,beta'-methylenedithiodialanine	Generator
Djenkolate	Generator
L-Djenkolate	Generator
Djenkolic acid, hydrochloride	MeSH

Chemical Formula

C₇H₁₄N₂O₄S₂

Average Mass

254.3200 Da

Monoisotopic Mass

254.03950 Da

IUPAC Name

(2R)-2-amino-3-[({[(2R)-2-amino-2-carboxyethyl]sulfanyl}methyl)sulfanyl]propanoic acid

Traditional Name

djenkolic acid

CAS Registry Number

Not Available

SMILES

N[C@@H](CSCSC[C@H](N)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C7H14N2O4S2/c8-4(6(10)11)1-14-3-15-2-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1

InChI Key

JMQMNWIBUCGUDO-WHFBIAKZSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Acacia spp.	Plant	KNApSAcK
Albizia lophantha	Plant	KNApSAcK
Archidendron bubalinum	LOTUS Database	35616633
Mimosa spp.	Plant	KNApSAcK
Pithecollobium bubalinum	-	KNApSAcK
Pithecolobium lobatum	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-cysteine-s-conjugates. L-cysteine-S-conjugates are compounds containing L-cysteine where the thio-group is conjugated.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-cysteine-S-conjugates

Alternative Parents

Substituents

L-cysteine-s-conjugate
Alpha-amino acid
L-alpha-amino acid
Dicarboxylic acid or derivatives
Thioacetal
Amino acid
Carboxylic acid
Thioether
Dialkylthioether
Sulfenyl compound
Organic nitrogen compound
Hydrocarbon derivative
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

non-proteinogenic L-alpha-amino acid (CHEBI:6211 )
L-cysteine derivative (CHEBI:6211 )
dithioacetal (CHEBI:6211 )

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	-3.8	ALOGPS
logP	-5.4	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	1.67	ChemAxon
pKa (Strongest Basic)	9.43	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	126.64 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	58.97 m³·mol⁻¹	ChemAxon
Polarizability	25.63 Å³	ChemAxon
Number of Rings	0	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

C00001356

Chemspider ID

61442

KEGG Compound ID

C08275

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Djenkolic_acid

METLIN ID

Not Available

PubChem Compound

68134

PDB ID

Not Available

ChEBI ID

6211

Good Scents ID

Not Available

References

General References

Kim J, Senadheera DB, Levesque CM, Cvitkovitch DG: TcyR regulates L-cystine uptake via the TcyABC transporter in Streptococcus mutans. FEMS Microbiol Lett. 2012 Mar;328(2):114-21. doi: 10.1111/j.1574-6968.2011.02492.x. Epub 2012 Jan 17. [PubMed:22212096 ]
Bulut H, Moniot S, Licht A, Scheffel F, Gathmann S, Saenger W, Schneider E: Crystal structures of two solute receptors for L-cystine and L-cysteine, respectively, of the human pathogen Neisseria gonorrhoeae. J Mol Biol. 2012 Jan 20;415(3):560-72. doi: 10.1016/j.jmb.2011.11.030. Epub 2011 Nov 23. [PubMed:22138345 ]
Burguiere P, Auger S, Hullo MF, Danchin A, Martin-Verstraete I: Three different systems participate in L-cystine uptake in Bacillus subtilis. J Bacteriol. 2004 Aug;186(15):4875-84. doi: 10.1128/JB.186.15.4875-4884.2004. [PubMed:15262924 ]
Elbetieha A, Owais WM, Saadoun I, Hussein E: Effect of glutathione L-cystein and L-djenkolic acid in the synthesis and mutagenicity of azide metabolite in Bacillus subtilis ATCC 6633 strain. New Microbiol. 1999 Oct;22(4):315-22. [PubMed:10555201 ]
RERABEK J: The deamination of djenkolic acid in rats. Experientia. 1950 Aug 15;6(8):304-5. doi: 10.1007/BF02170908. [PubMed:15435518 ]

Showing NP-Card for Djenkolic acid (NP0050677)

MOL for NP0050677 (Djenkolic acid)

3D MOL for NP0050677 (Djenkolic acid)

3D SDF for NP0050677 (Djenkolic acid)

3D-SDF for NP0050677 (Djenkolic acid)

PDB for NP0050677 (Djenkolic acid)

3D PDB for NP0050677 (Djenkolic acid)

SMILES for NP0050677 (Djenkolic acid)

INCHI for NP0050677 (Djenkolic acid)

Structure for NP0050677 (Djenkolic acid)

3D Structure for NP0050677 (Djenkolic acid)