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Showing metabocard for Nitrilotriacetic acid (HMDB0255635)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 15:25:09 UTC
Update Date2021-09-26 23:10:38 UTC
HMDB IDHMDB0255635
Secondary Accession NumbersNone
Metabolite Identification
Common NameNitrilotriacetic acid
DescriptionNitrilotriacetic acid, also known as nitrilotriacetate or H3NTA, 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). The his-tag binds the metal of metal chelator complexes. Despite widespread use in cleaning products, the concentration in the water supply is too low to have a sizeable impact on human health or environmental quality. Nitrilotriacetic acid is a very strong basic compound (based on its pKa). Nitrilotriacetic acid is formally rated as a possible carcinogen (by IARC 2B) and is also a potentially toxic compound. In one application, NTA as a chelating agent removes Cr, Cu, and As from wood that had been treated with chromated copper arsenate. NTA is a tripodal tetradentate trianionic ligand. This compound has been identified in human blood as reported by (PMID: 31557052 ). Nitrilotriacetic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Nitrilotriacetic acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0255635 (Nitrilotriacetic acid)

  Mrv0541 02231216382D          

 13 12  0  0  0  0            999 V2000
    1.4289   -4.7289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -3.9039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.4914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0934   -0.6753    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  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
  7  9  2  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
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3D MOL for HMDB0255635 (Nitrilotriacetic acid)

HMDB0255635
     RDKit          3D
Nitrilotriacetic acid
 22 21  0  0  0  0  0  0  0  0999 V2000
    0.7364    2.7303    1.6288 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0788    2.0584    0.7966 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5336    2.7734   -0.2465 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1192    0.6066    0.8103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1566   -0.0276   -0.4754 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8139   -1.3575   -0.3469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2383   -1.2644   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7805   -0.1214    0.0665 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0499   -2.3697    0.0285 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1898   -0.4520   -0.9163 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1359    0.5598   -1.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9221    1.7556   -1.3889 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4676    0.1412   -1.4939 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5501    2.9098   -0.2682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0324    0.3986    1.4429 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7082    0.1846    1.4582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2970   -1.9052    0.4930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5564   -1.9003   -1.2719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8402   -2.5748   -0.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9949   -1.0940   -1.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5728   -1.1952   -0.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1617    0.1441   -0.7313 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  5 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  6 17  1  0
  6 18  1  0
  9 19  1  0
 10 20  1  0
 10 21  1  0
 13 22  1  0
M  END
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3D SDF for HMDB0255635 (Nitrilotriacetic acid)

  Mrv0541 02231216382D          

 13 12  0  0  0  0            999 V2000
    1.4289   -4.7289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -3.9039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.4914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0934   -0.6753    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  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
  7  9  2  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255635

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CN(CC(O)=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO6/c8-4(9)1-7(2-5(10)11)3-6(12)13/h1-3H2,(H,8,9)(H,10,11)(H,12,13)

> <INCHI_KEY>
MGFYIUFZLHCRTH-UHFFFAOYSA-N

> <FORMULA>
C6H9NO6

> <MOLECULAR_WEIGHT>
191.1388

> <EXACT_MASS>
191.042987025

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
16.124303620770064

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.98

> <JCHEM_LOGP>
-2.0884216896573173

> <ALOGPS_LOGS>
-0.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.681643741218178

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7801441046489845

> <JCHEM_PKA_STRONGEST_BASIC>
5.580483974493386

> <JCHEM_POLAR_SURFACE_AREA>
115.14000000000001

> <JCHEM_REFRACTIVITY>
38.2419

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.17e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nitrilotriacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0255635 (Nitrilotriacetic acid)

HMDB0255635
     RDKit          3D
Nitrilotriacetic acid
 22 21  0  0  0  0  0  0  0  0999 V2000
    0.7364    2.7303    1.6288 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0788    2.0584    0.7966 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5336    2.7734   -0.2465 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1192    0.6066    0.8103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1566   -0.0276   -0.4754 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8139   -1.3575   -0.3469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2383   -1.2644   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7805   -0.1214    0.0665 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0499   -2.3697    0.0285 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1898   -0.4520   -0.9163 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1359    0.5598   -1.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9221    1.7556   -1.3889 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4676    0.1412   -1.4939 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5501    2.9098   -0.2682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0324    0.3986    1.4429 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7082    0.1846    1.4582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2970   -1.9052    0.4930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5564   -1.9003   -1.2719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8402   -2.5748   -0.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9949   -1.0940   -1.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5728   -1.1952   -0.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1617    0.1441   -0.7313 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  5 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  6 17  1  0
  6 18  1  0
  9 19  1  0
 10 20  1  0
 10 21  1  0
 13 22  1  0
M  END
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PDB for HMDB0255635 (Nitrilotriacetic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       2.667  -8.827   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -7.287   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.001  -6.517   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -6.517   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.334  -4.977   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.000  -4.207   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334  -1.897   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.334  -1.897   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667  -4.207   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -2.667   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.041  -1.261   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.001  -1.897   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    5   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0255635 (Nitrilotriacetic acid)

COMPND    HMDB0255635
HETATM    1  O1  UNL     1       0.736   2.730   1.629  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.079   2.058   0.797  1.00  0.00           C  
HETATM    3  O2  UNL     1      -0.534   2.773  -0.247  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.119   0.607   0.810  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.157  -0.028  -0.475  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.814  -1.358  -0.347  1.00  0.00           C  
HETATM    7  C4  UNL     1      -2.238  -1.264  -0.078  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.780  -0.121   0.066  1.00  0.00           O  
HETATM    9  O4  UNL     1      -3.050  -2.370   0.029  1.00  0.00           O  
HETATM   10  C5  UNL     1       1.190  -0.452  -0.916  1.00  0.00           C  
HETATM   11  C6  UNL     1       2.136   0.560  -1.265  1.00  0.00           C  
HETATM   12  O5  UNL     1       1.922   1.756  -1.389  1.00  0.00           O  
HETATM   13  O6  UNL     1       3.468   0.141  -1.494  1.00  0.00           O  
HETATM   14  H1  UNL     1      -1.550   2.910  -0.268  1.00  0.00           H  
HETATM   15  H2  UNL     1      -1.032   0.399   1.443  1.00  0.00           H  
HETATM   16  H3  UNL     1       0.708   0.185   1.458  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.297  -1.905   0.493  1.00  0.00           H  
HETATM   18  H5  UNL     1      -0.556  -1.900  -1.272  1.00  0.00           H  
HETATM   19  H6  UNL     1      -3.840  -2.575  -0.578  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.995  -1.094  -1.842  1.00  0.00           H  
HETATM   21  H8  UNL     1       1.573  -1.195  -0.155  1.00  0.00           H  
HETATM   22  H9  UNL     1       4.162   0.144  -0.731  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6   10
CONECT    6    7   17   18
CONECT    7    8    8    9
CONECT    9   19
CONECT   10   11   20   21
CONECT   11   12   12   13
CONECT   13   22
END
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SMILES for HMDB0255635 (Nitrilotriacetic acid)

OC(=O)CN(CC(O)=O)CC(O)=O
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INCHI for HMDB0255635 (Nitrilotriacetic acid)

InChI=1S/C6H9NO6/c8-4(9)1-7(2-5(10)11)3-6(12)13/h1-3H2,(H,8,9)(H,10,11)(H,12,13)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H9NO6
Average Molecular Weight191.1388
Monoisotopic Molecular Weight191.042987025
IUPAC Name2-[bis(carboxymethyl)amino]acetic acid
Traditional Namenitrilotriacetic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CN(CC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C6H9NO6/c8-4(9)1-7(2-5(10)11)3-6(12)13/h1-3H2,(H,8,9)(H,10,11)(H,12,13)
InChI KeyMGFYIUFZLHCRTH-UHFFFAOYSA-N
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
  • Tricarboxylic acid or derivatives
  • Tertiary amine
  • Tertiary aliphatic amine
  • Amino acid
  • Carboxylic acid
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03040
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC14695
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNitrilotriacetic acid
METLIN IDNot Available
PubChem Compound8758
PDB IDNot Available
ChEBI ID44557
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]