NP-MRD: Showing NP-Card for Hydroxyprolyl-Arginine (NP0136470)

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Record Information

Version

2.0

Created at

2022-05-12 15:15:22 UTC

Updated at

2022-05-12 15:15:22 UTC

NP-MRD ID

NP0136470

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hydroxyprolyl-Arginine

Description

Hydroxyprolyl-Arginine, also known as HP-R dipeptide or hpro-arg, belongs to the class of organic compounds known as peptides. Peptides are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another. Some dipeptides are known to have physiological or cell-signaling effects although most are simply short-lived intermediates on their way to specific amino acid degradation pathways following further proteolysis. Hydroxyprolyl-Arginine is a dipeptide composed of hydroxyproline and arginine. Hydroxyprolyl-Arginine is a very strong basic compound (based on its pKa). It is an incomplete breakdown product of protein digestion or protein catabolism. This dipeptide has not yet been identified in human tissues or biofluids and so it is classified as an 'Expected' metabolite.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 41 41  0  0  0  0  0  0  0  0999 V2000
    4.8811   -0.1703   -3.0076 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9073    0.6807   -2.4097 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5978    0.5972   -1.1663 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6464    1.7827   -0.3859 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2239   -0.6532   -0.6220 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0491   -0.8803    0.7919 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8392   -0.1340    1.3473 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6053   -0.5868    0.6524 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3962    0.1519    1.1668 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7312   -0.3760    0.4008 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5362    0.4324   -0.4212 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3002    1.6508   -0.5174 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6603   -0.1513   -1.1715 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7229   -0.7291   -0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0543   -0.4730   -0.9323 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.8003    0.4308   -0.1754 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6150    0.1460   -2.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3758    0.8357   -1.9544 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1555   -0.1618    2.5877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8849   -0.8353    2.8924 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0048    0.2417    3.6097 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3929    1.9356    0.3234 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9268    2.5526   -0.4963 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0559   -1.4829   -1.2563 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9277   -1.9439    1.0400 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9615   -0.5330    1.3180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9530    0.9407    1.2139 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8131   -0.4110    2.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3899   -1.6808    0.8300 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6463   -0.3904   -0.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5114    1.2440    0.9911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9216   -1.3833    0.4849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3343   -0.9505   -1.8700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6146   -0.2533    0.7180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5149   -1.8126   -0.1587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5685   -1.4318   -1.0819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4704   -0.0716    0.3632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3898    0.8276   -2.6650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4184   -0.7125   -2.9471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5890    1.6884   -1.4306 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6173    0.5276    4.5121 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0
  3  2  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  9 19  1  0
 19 21  1  0
 19 20  2  0
 18 13  1  0
  4 22  1  0
  4 23  1  0
  2  1  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
  8 29  1  0
  8 30  1  0
  9 31  1  1
 10 32  1  0
 13 33  1  6
 14 34  1  0
 14 35  1  0
 15 36  1  6
 16 37  1  0
 17 38  1  0
 17 39  1  0
 18 40  1  0
 21 41  1  0
M  END


  Mrv1652304062013432D          

 20 20  0  0  0  0            999 V2000
    0.4875   -1.6527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2269   -1.2402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2269   -0.4152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9414   -1.6527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0277   -2.4731    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8346   -2.6447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2471   -1.9302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0676   -1.8440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6951   -1.3171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2020   -1.2402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9165   -1.6527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6309   -1.2402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3454   -1.6527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0599   -1.2402    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7744   -1.6527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4888   -1.2402    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7744   -2.4777    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2020   -0.4152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9165   -0.0027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4875   -0.0027    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  1  0  0  0  0
  4  9  1  0  0  0  0
  1 10  1  0  0  0  0
 10 11  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
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 10 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0136470

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(=N)NCCCC(NC(=O)C1CC(O)CN1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H21N5O4/c12-11(13)14-3-1-2-7(10(19)20)16-9(18)8-4-6(17)5-15-8/h6-8,15,17H,1-5H2,(H,16,18)(H,19,20)(H4,12,13,14)

> <INCHI_KEY>
AZDCVMCXGLWYHN-UHFFFAOYSA-N

> <FORMULA>
C11H21N5O4

> <MOLECULAR_WEIGHT>
287.3155

> <EXACT_MASS>
287.159354185

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
29.272014616259984

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-carbamimidamido-2-[(4-hydroxypyrrolidin-2-yl)formamido]pentanoic acid

> <ALOGPS_LOGP>
-3.30

> <JCHEM_LOGP>
-4.378228038581765

> <ALOGPS_LOGS>
-2.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.561152919370159

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.51619828704424

> <JCHEM_PKA_STRONGEST_BASIC>
12.05360420830799

> <JCHEM_POLAR_SURFACE_AREA>
160.55999999999997

> <JCHEM_REFRACTIVITY>
80.10539999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.28e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-carbamimidamido-2-[(4-hydroxypyrrolidin-2-yl)formamido]pentanoic 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  N   UNK     0       0.910  -3.085   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -0.424  -2.315   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.424  -0.775   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.757  -3.085   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -1.918  -4.616   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -3.425  -4.937   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.195  -3.603   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -5.726  -3.442   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -3.164  -2.459   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.244  -2.315   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.577  -3.085   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.911  -2.315   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.245  -3.085   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       7.578  -2.315   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       8.912  -3.085   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      10.246  -2.315   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       8.912  -4.625   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       2.244  -0.775   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.577  -0.005   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.910  -0.005   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    4                                                       
CONECT   10    1   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   10   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Value	Source
Hydroxyproline arginine dipeptide	HMDB
HP-R Dipeptide	HMDB
HPR Dipeptide	HMDB
Hpro-arg	HMDB
Hydroxyproline-arginine dipeptide	HMDB
Hydroxyprolylarginine	HMDB
L-Hydroxyprolyl-L-arginine	HMDB
5-Carbamimidamido-2-{[hydroxy(4-hydroxypyrrolidin-2-yl)methylidene]amino}pentanoate	Generator

Chemical Formula

C₁₁H₂₁N₅O₄

Average Mass

287.3155 Da

Monoisotopic Mass

287.15935 Da

IUPAC Name

5-carbamimidamido-2-[(4-hydroxypyrrolidin-2-yl)formamido]pentanoic acid

Traditional Name

5-carbamimidamido-2-[(4-hydroxypyrrolidin-2-yl)formamido]pentanoic acid

CAS Registry Number

Not Available

SMILES

NC(=N)NCCCC(NC(=O)C1CC(O)CN1)C(O)=O

InChI Identifier

InChI=1S/C11H21N5O4/c12-11(13)14-3-1-2-7(10(19)20)16-9(18)8-4-6(17)5-15-8/h6-8,15,17H,1-5H2,(H,16,18)(H,19,20)(H4,12,13,14)

InChI Key

AZDCVMCXGLWYHN-UHFFFAOYSA-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 peptides. Peptides are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Peptides

Alternative Parents

Substituents

Alpha peptide
Isoleucine or derivatives
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid or derivatives
Branched fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Fatty acyl
Fatty acid
Pyrrolidine
1,2-aminoalcohol
Amino acid or derivatives
Amino acid
Secondary alcohol
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid
Secondary aliphatic amine
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Secondary amine
Organic oxygen compound
Hydrocarbon derivative
Amine
Organopnictogen compound
Organic oxide
Carbonyl group
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-3.3	ALOGPS
logP	-4.4	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	3.52	ChemAxon
pKa (Strongest Basic)	12.05	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	160.56 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	80.11 m³·mol⁻¹	ChemAxon
Polarizability	29.27 Å³	ChemAxon
Number of Rings	1	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

HMDB0028857

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

131750764

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Hydroxyprolyl-Arginine (NP0136470)

MOL for NP0136470 (Hydroxyprolyl-Arginine)

3D MOL for NP0136470 (Hydroxyprolyl-Arginine)

3D SDF for NP0136470 (Hydroxyprolyl-Arginine)

3D-SDF for NP0136470 (Hydroxyprolyl-Arginine)

PDB for NP0136470 (Hydroxyprolyl-Arginine)

3D PDB for NP0136470 (Hydroxyprolyl-Arginine)

SMILES for NP0136470 (Hydroxyprolyl-Arginine)

INCHI for NP0136470 (Hydroxyprolyl-Arginine)

Structure for NP0136470 (Hydroxyprolyl-Arginine)

3D Structure for NP0136470 (Hydroxyprolyl-Arginine)