Np mrd loader

Showing NP-Card for gamma-Carboxyglutamic acid (NP0136262)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-05-12 15:09:58 UTC
Updated at2022-05-12 15:09:58 UTC
NP-MRD IDNP0136262
Secondary Accession NumbersNone
Natural Product Identification
Common Namegamma-Carboxyglutamic acid
DescriptionGamma-Carboxyglutamic acid, also known as g-carboxyglutamate, 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). In the blood coagulation cascade, Vitamin K is required to introduce gamma-carboxylation of clotting factors II, VII, IX, X and protein Z. Carboxyglutamic acid (or the conjugate base, carboxyglutamate), is an uncommon amino acid introduced into proteins by a post-translational carboxylation of glutamic acid residues. Gamma-Carboxyglutamic acid is a very strong basic compound (based on its pKa). This modification is found, for example, in clotting factors and other proteins of the coagulation cascade. This modification introduces an affinity for calcium ions.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0136262 (gamma-Carboxyglutamic acid)


  Mrv1652304062013062D          

 13 12  0  0  0  0            999 V2000
    3.7125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
M  END
Download

3D MOL for NP0136262 (gamma-Carboxyglutamic acid)

     RDKit          3D

 22 21  0  0  0  0  0  0  0  0999 V2000
    1.9747   -1.8535    0.4167 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3570   -0.4948    0.4753 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0575   -0.7239    0.1243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0000    0.4041    0.0477 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7736    1.4367   -0.9457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1296    1.1785   -1.9903 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2465    2.7308   -0.8063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3628   -0.2091   -0.2000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9931    0.0853   -1.2221 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8825   -1.1042    0.7441 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1723    0.3448   -0.3947 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9006   -0.1271   -1.2978 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1594    1.7213   -0.2279 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6516   -2.2667   -0.4836 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5223   -2.4051    1.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4976   -0.1890    1.5490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0938   -1.2877   -0.8403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4862   -1.4485    0.8881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1076    0.8136    1.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7519    3.0493    0.0003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2908   -1.9705    0.4154 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9403    2.3159   -0.3869 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  7  1  0
  5  6  2  0
  4  8  1  0
  8 10  1  0
  8  9  2  0
  2 11  1  0
 11 13  1  0
 11 12  2  0
  1 14  1  0
  1 15  1  0
  2 16  1  1
  3 17  1  0
  3 18  1  0
  4 19  1  1
  7 20  1  0
 10 21  1  0
 13 22  1  0
M  END
Download

3D SDF for NP0136262 (gamma-Carboxyglutamic acid)


  Mrv1652304062013062D          

 13 12  0  0  0  0            999 V2000
    3.7125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0136262

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CC(C(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO6/c7-3(6(12)13)1-2(4(8)9)5(10)11/h2-3H,1,7H2,(H,8,9)(H,10,11)(H,12,13)

> <INCHI_KEY>
UHBYWPGGCSDKFX-UHFFFAOYSA-N

> <FORMULA>
C6H9NO6

> <MOLECULAR_WEIGHT>
191.1388

> <EXACT_MASS>
191.042987025

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
16.24164659895778

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-aminopropane-1,3,3-tricarboxylic acid

> <ALOGPS_LOGP>
-3.02

> <JCHEM_LOGP>
-3.6276420554601425

> <ALOGPS_LOGS>
-0.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.606856873434833

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.476846937636764

> <JCHEM_PKA_STRONGEST_BASIC>
9.537788074343204

> <JCHEM_POLAR_SURFACE_AREA>
137.92000000000002

> <JCHEM_REFRACTIVITY>
37.57940000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.25e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
carboxyglutamic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0136262 (gamma-Carboxyglutamic acid)

Download
PDB for NP0136262 (gamma-Carboxyglutamic acid)
HEADER    PROTEIN                                 06-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-APR-20         0                                  
HETATM    1  C   UNK     0       6.930  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.390  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.700   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.620   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.240   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       6.930   1.334   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       3.080  -2.667   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       5.390  -4.001   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.080   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.390   1.334   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      10.010   1.334   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      10.010  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4    5                                                  
CONECT    3    1    6    7                                                  
CONECT    4    2    8    9                                                  
CONECT    5    2   10   11                                                  
CONECT    6    3   12   13                                                  
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Download
3D PDB for NP0136262 (gamma-Carboxyglutamic acid)
Download
SMILES for NP0136262 (gamma-Carboxyglutamic acid)
NC(CC(C(O)=O)C(O)=O)C(O)=O
Download
INCHI for NP0136262 (gamma-Carboxyglutamic acid)
InChI=1S/C6H9NO6/c7-3(6(12)13)1-2(4(8)9)5(10)11/h2-3H,1,7H2,(H,8,9)(H,10,11)(H,12,13)
Download
View in JSmol
Synonyms
ValueSource
g-CarboxyglutamateGenerator
g-Carboxyglutamic acidGenerator
gamma-CarboxyglutamateGenerator
Γ-carboxyglutamateGenerator
Γ-carboxyglutamic acidGenerator
1-Carboxyglutamic acidHMDB
3-Amino-1,1,3-propanetricarboxylic acidHMDB
1 Carboxyglutamic acidHMDB
gamma CarboxyglutamateHMDB
gamma Carboxyglutamic acidHMDB
1-Aminopropane-1,3,3-tricarboxylateGenerator
gamma-Carboxyglutamic acidMeSH
Chemical FormulaC6H9NO6
Average Mass191.1388 Da
Monoisotopic Mass191.04299 Da
IUPAC Name1-aminopropane-1,3,3-tricarboxylic acid
Traditional Namecarboxyglutamic acid
CAS Registry NumberNot Available
SMILES
NC(CC(C(O)=O)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C6H9NO6/c7-3(6(12)13)1-2(4(8)9)5(10)11/h2-3H,1,7H2,(H,8,9)(H,10,11)(H,12,13)
InChI KeyUHBYWPGGCSDKFX-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 OriginNot Available
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
    • 

  • Amino fatty acid
    • 

  • 1,3-dicarbonyl compound
    • 

  • Fatty acyl
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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-3ALOGPS
logP-3.6ChemAxon
logS-0.93ALOGPS
pKa (Strongest Acidic)1.48ChemAxon
pKa (Strongest Basic)9.54ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area137.92 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.58 m³·mol⁻¹ChemAxon
Polarizability16.24 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0041900  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID37241  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCarboxyglutamic acid  
METLIN IDNot Available
PubChem Compound40772  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available