NP-MRD: Showing NP-Card for Arginylglycine (NP0136348)

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Record Information

Version

2.0

Created at

2022-05-12 15:12:16 UTC

Updated at

2022-05-12 15:12:16 UTC

NP-MRD ID

NP0136348

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Arginylglycine

Description

Arginylglycine, also known as arg-gly or R-g dipeptide, belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Arginylglycine is a very strong basic compound (based on its pKa). It is an incomplete breakdown product of protein digestion or protein catabolism.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 32  0  0  0  0  0  0  0  0999 V2000
    4.8848   -1.3702   -1.6372 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9507   -0.3334   -1.6820 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1317    0.4681   -1.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3260    1.8609   -1.2239 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0779   -0.0727   -0.3259 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8382   -0.4160   -0.9624 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8190   -0.9817   -0.0027 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4717   -0.0114    1.0962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5380   -0.5538    2.0592 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1288   -1.7429    2.7340 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8697   -0.7391    1.4350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4599   -1.8425    1.5544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5222    0.2817    0.6983 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8154    0.1055    0.0907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2360    1.3434   -0.6091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4971    2.3808   -0.6251 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4507    1.4038   -1.2673 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5387    2.4195   -1.6400 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1718    2.3816   -0.9521 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2033   -0.2187    0.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3995    0.4722   -1.5068 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0713   -1.1454   -1.7649 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1902   -1.9396    0.3655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1064   -1.1769   -0.5841 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0502    0.9211    0.6660 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4005    0.2885    1.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6778    0.2383    2.8489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9370   -2.0813    3.3037 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1471   -2.5201    2.1113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0436    1.1971    0.5935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7368   -0.7091   -0.6669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6027   -0.1240    0.8467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0505    2.2163   -1.1475 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 17  1  0
 15 16  2  0
 10 28  1  0
 10 29  1  0
  9 27  1  1
  8 25  1  0
  8 26  1  0
  7 23  1  0
  7 24  1  0
  6 21  1  0
  6 22  1  0
  5 20  1  0
  4 18  1  0
  4 19  1  0
  2  1  1  0
 13 30  1  0
 14 31  1  0
 14 32  1  0
 17 33  1  0
M  END


  Mrv1652304062013222D          

 16 15  0  0  0  0            999 V2000
 2501.0723 2500.2058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2500.3574 2499.7941    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 2499.6425 2500.2058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.9276 2499.7941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.2124 2500.2058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2497.4975 2499.7941    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2496.7826 2500.2058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2496.7826 2501.0315    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2496.0677 2499.7941    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2500.3574 2498.9684    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2501.7875 2499.7941    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2502.5024 2500.2058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2503.2173 2499.7941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2503.9322 2500.2058    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2503.2173 2498.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.0723 2501.0315    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 11  1  0  0  0  0
  1 16  2  0  0  0  0
  2  3  1  0  0  0  0
  2 10  1  1  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  2  0  0  0  0
  7  9  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0136348

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H17N5O3/c9-5(2-1-3-12-8(10)11)7(16)13-4-6(14)15/h5H,1-4,9H2,(H,13,16)(H,14,15)(H4,10,11,12)/t5-/m0/s1

> <INCHI_KEY>
XUUXCWCKKCZEAW-YFKPBYRVSA-N

> <FORMULA>
C8H17N5O3

> <MOLECULAR_WEIGHT>
231.256

> <EXACT_MASS>
231.133139427

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.298877401582633

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2S)-2-amino-5-carbamimidamidopentanamido]acetic acid

> <ALOGPS_LOGP>
-3.67

> <JCHEM_LOGP>
-4.247337778645383

> <ALOGPS_LOGS>
-2.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.399957843463898

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6284069214820334

> <JCHEM_PKA_STRONGEST_BASIC>
12.12634404454537

> <JCHEM_POLAR_SURFACE_AREA>
154.32

> <JCHEM_REFRACTIVITY>
66.72659999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.35e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2S)-2-amino-5-carbamimidamidopentanamido]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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    4668.6684667.051   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    4667.3344666.282   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    4665.9994667.051   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    4664.6654666.282   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    4663.3304667.051   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    4661.9954666.282   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    4660.6614667.051   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0    4660.6614668.592   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0    4659.3264666.282   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0    4667.3344664.741   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0    4670.0034666.282   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0    4671.3384667.051   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    4672.6724666.282   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0    4674.0074667.051   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0    4672.6724664.741   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0    4668.6684668.592   0.000  0.00  0.00           O+0
CONECT    1    2   11   16                                                  
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    2                                                            
CONECT   11    1   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    1                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

View in JSmol

Synonyms

Value	Source
2-{[(2S)-2-amino-5-carbamimidamido-1-hydroxypentylidene]amino}acetate	HMDB
Arg-gly	HMDB
Arginine glycine dipeptide	HMDB
Arginine-glycine dipeptide	HMDB
Arginyl-glycine	HMDB
L-Arg-gly	HMDB
L-Arginylglycine	HMDB
N-Arginylglycine	HMDB
N-L-Arginylglycine	HMDB
R-g Dipeptide	HMDB
RG Dipeptide	HMDB

Chemical Formula

C₈H₁₇N₅O₃

Average Mass

231.2560 Da

Monoisotopic Mass

231.13314 Da

IUPAC Name

2-[(2S)-2-amino-5-carbamimidamidopentanamido]acetic acid

Traditional Name

[(2S)-2-amino-5-carbamimidamidopentanamido]acetic acid

CAS Registry Number

Not Available

SMILES

N[C@@H](CCCNC(N)=N)C(=O)NCC(O)=O

InChI Identifier

InChI=1S/C8H17N5O3/c9-5(2-1-3-12-8(10)11)7(16)13-4-6(14)15/h5H,1-4,9H2,(H,13,16)(H,14,15)(H4,10,11,12)/t5-/m0/s1

InChI Key

XUUXCWCKKCZEAW-YFKPBYRVSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Alpha-amino acid or derivatives
Fatty amide
Fatty acyl
N-acyl-amine
Amino acid or derivatives
Carboxamide group
Amino acid
Guanidine
Secondary carboxylic acid amide
Carboxylic acid
Organic 1,3-dipolar compound
Monocarboxylic acid or derivatives
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Organic oxygen compound
Primary aliphatic amine
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Amine
Organopnictogen compound
Primary amine
Organonitrogen compound
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

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	-3.7	ALOGPS
logP	-4.2	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	3.63	ChemAxon
pKa (Strongest Basic)	12.13	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	154.32 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	66.73 m³·mol⁻¹	ChemAxon
Polarizability	23.3 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0028709

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

142765

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Arginylglycine (NP0136348)

MOL for NP0136348 (Arginylglycine)

3D MOL for NP0136348 (Arginylglycine)

3D SDF for NP0136348 (Arginylglycine)

3D-SDF for NP0136348 (Arginylglycine)

PDB for NP0136348 (Arginylglycine)

3D PDB for NP0136348 (Arginylglycine)

SMILES for NP0136348 (Arginylglycine)

INCHI for NP0136348 (Arginylglycine)

Structure for NP0136348 (Arginylglycine)

3D Structure for NP0136348 (Arginylglycine)