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Showing NP-Card for Iminodiacetic acid (NP0084115)

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Record Information
Version1.0
Created at2022-04-29 04:56:55 UTC
Updated at2022-04-29 04:56:55 UTC
NP-MRD IDNP0084115
Secondary Accession NumbersNone
Natural Product Identification
Common NameIminodiacetic acid
DescriptionIminodiacetic acid, also known as 2,2'-iminodiacetate or diglycine, belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). An amino dicarboxylic acid that is glycine in which one of the hydrogens attached to the nitrogen is substituted by a carboxymethyl group. Iminodiacetic acid is found in Pogostemon cablin and Triticum aestivum . It was first documented in 1992 (PMID: 1735711). Iminodiacetic acid is a very strong basic compound (based on its pKa) (PMID: 21212492) (PMID: 21488608) (PMID: 21567989) (PMID: 8892809).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0084115 (Iminodiacetic acid)


  Mrv0541 02241201532D          

  9  8  0  0  0  0            999 V2000
   11.7612   -7.4524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7612   -6.6274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0467   -7.8649    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.4757   -7.8649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1902   -7.4524    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.6191   -7.4524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6191   -6.6274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3336   -7.8649    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9047   -7.8649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  1  0  0  0  0
  9  6  1  0  0  0  0
  5  9  1  0  0  0  0
M  END
Download

3D MOL for NP0084115 (Iminodiacetic acid)

     RDKit          3D

 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.1962   -0.5111   -1.8715 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0038   -0.0085   -0.7828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5279    1.2420   -0.5590 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2332   -0.7161    0.2195 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0079    0.0204    0.5467 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9358    0.2761   -0.4405 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2068   -0.3354   -0.1847 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2796   -1.5247    0.1575 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3801    0.3546   -0.3116 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3977    1.4406   -0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8678   -0.6690    1.1830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1127   -1.7716    0.0266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4390   -0.5779    1.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1008    1.4089   -0.5125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5435    0.0297   -1.4548 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4455    1.3420   -0.5791 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  9  1  0
  7  8  2  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
  9 16  1  0
M  END
Download

3D SDF for NP0084115 (Iminodiacetic acid)


  Mrv0541 02241201532D          

  9  8  0  0  0  0            999 V2000
   11.7612   -7.4524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7612   -6.6274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0467   -7.8649    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.4757   -7.8649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1902   -7.4524    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.6191   -7.4524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6191   -6.6274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3336   -7.8649    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9047   -7.8649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  1  0  0  0  0
  9  6  1  0  0  0  0
  5  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084115

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CNCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H7NO4/c6-3(7)1-5-2-4(8)9/h5H,1-2H2,(H,6,7)(H,8,9)

> <INCHI_KEY>
NBZBKCUXIYYUSX-UHFFFAOYSA-N

> <FORMULA>
C4H7NO4

> <MOLECULAR_WEIGHT>
133.1027

> <EXACT_MASS>
133.037507717

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
11.626095003093472

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(carboxymethyl)amino]acetic acid

> <ALOGPS_LOGP>
-2.50

> <JCHEM_LOGP>
-4.06804657078968

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.895899041436653

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.122315742053777

> <JCHEM_PKA_STRONGEST_BASIC>
8.797441854574897

> <JCHEM_POLAR_SURFACE_AREA>
86.63000000000001

> <JCHEM_REFRACTIVITY>
26.8626

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.69e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
iminodiacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0084115 (Iminodiacetic acid)

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PDB for NP0084115 (Iminodiacetic acid)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      21.954 -13.911   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      21.954 -12.371   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      20.621 -14.681   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      23.288 -14.681   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      24.622 -13.911   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      27.289 -13.911   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      27.289 -12.371   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      28.623 -14.681   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      25.955 -14.681   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5                                                       
CONECT    5    4    9                                                       
CONECT    6    7    8    9                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6    5                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0084115 (Iminodiacetic acid)
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SMILES for NP0084115 (Iminodiacetic acid)
OC(=O)CNCC(O)=O
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INCHI for NP0084115 (Iminodiacetic acid)
InChI=1S/C4H7NO4/c6-3(7)1-5-2-4(8)9/h5H,1-2H2,(H,6,7)(H,8,9)
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Synonyms
ValueSource
2,2'-Iminodiacetic acidChEBI
Aminodiacetic acidChEBI
Bis(carboxymethyl)amineChEBI
DiglycineChEBI
DiglycocollChEBI
IDAChEBI
Iminobis(acetic acid)ChEBI
Iminodiethanoic acidChEBI
N-(Carboxymethyl)glycineChEBI
2,2'-IminodiacetateGenerator
AminodiacetateGenerator
Iminobis(acetate)Generator
IminodiethanoateGenerator
IminodiacetateGenerator
N-(Carboxymethyl)- glycineHMDB
Iminodiacetic acid, calcium salt (1:1)HMDB
Iminodiacetic acid, sodium saltHMDB
Imidodiacetic acidHMDB
Iminodiacetic acid, disodium saltHMDB
Iminodiacetic acidGenerator
Chemical FormulaC4H7NO4
Average Mass133.1027 Da
Monoisotopic Mass133.03751 Da
IUPAC Name2-[(carboxymethyl)amino]acetic acid
Traditional Nameiminodiacetic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CNCC(O)=O
InChI Identifier
InChI=1S/C4H7NO4/c6-3(7)1-5-2-4(8)9/h5H,1-2H2,(H,6,7)(H,8,9)
InChI KeyNBZBKCUXIYYUSX-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Pogostemon cablinLOTUS Database
Triticum aestivumPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids  
Alternative Parents
Substituents
  • Alpha-amino acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Secondary amine
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.5ALOGPS
logP-4.1ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)2.12ChemAxon
pKa (Strongest Basic)8.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.63 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity26.86 m³·mol⁻¹ChemAxon
Polarizability11.63 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0011753  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028424  
KNApSAcK IDNot Available
Chemspider ID8557  
KEGG Compound IDC19911  
BioCyc IDCPD-10189  
BiGG IDNot Available
Wikipedia LinkIminodiacetic acid  
METLIN IDNot Available
PubChem Compound8897  
PDB IDNot Available
ChEBI ID24786  
Good Scents IDNot Available
References
General References
  1. Uetz T, Schneider R, Snozzi M, Egli T: Purification and characterization of a two-component monooxygenase that hydroxylates nitrilotriacetate from "Chelatobacter" strain ATCC 29600. J Bacteriol. 1992 Feb;174(4):1179-88. doi: 10.1128/jb.174.4.1179-1188.1992. [PubMed:1735711  ] 
  2. Zhang M, He X, Chen L, Zhang Y: Preparation and characterization of iminodiacetic acid-functionalized magnetic nanoparticles and its selective removal of bovine hemoglobin. Nanotechnology. 2011 Feb 11;22(6):065705. doi: 10.1088/0957-4484/22/6/065705. Epub 2011 Jan 7. [PubMed:21212492  ] 
  3. Zhang X, Kong X, Fan W, Du X: Iminodiacetic acid-functionalized gold nanoparticles for optical sensing of myoglobin via Cu2+ coordination. Langmuir. 2011 May 17;27(10):6504-10. doi: 10.1021/la200177e. Epub 2011 Apr 13. [PubMed:21488608  ] 
  4. Liu ZQ, Li FF, Cheng F, Zhang T, You ZY, Xu JM, Xue YP, Zheng YG, Shen YC: A novel synthesis of iminodiacetic acid: biocatalysis by whole Alcaligenes faecalis ZJB-09133 cells from iminodiacetonitrile. Biotechnol Prog. 2011 May-Jun;27(3):698-705. doi: 10.1002/btpr.603. Epub 2011 May 12. [PubMed:21567989  ] 
  5. Knobel HR, Egli T, van der Meer JR: Cloning and characterization of the genes encoding nitrilotriacetate monooxygenase of Chelatobacter heintzii ATCC 29600. J Bacteriol. 1996 Nov;178(21):6123-32. doi: 10.1128/jb.178.21.6123-6132.1996. [PubMed:8892809  ]