NP-MRD: Showing NP-Card for Hydroxyprolyl-Serine (NP0136481)

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Record Information

Version

2.0

Created at

2022-05-12 15:15:38 UTC

Updated at

2022-05-12 15:15:38 UTC

NP-MRD ID

NP0136481

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hydroxyprolyl-Serine

Description

Hydroxyprolyl-Serine, also known as HP-S dipeptide or hpro-ser, 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. Hydroxyprolyl-Serine is a very strong basic compound (based on its pKa). It is an incomplete breakdown product of protein digestion or protein catabolism. 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-Serine is a dipeptide composed of hydroxyproline and serine. Hydroxyprolyl-Serine was first documented in 2000 (PMID: 10900226). 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

 29 29  0  0  0  0  0  0  0  0999 V2000
   -2.1699    0.6993   -2.2367 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9458    0.1939   -1.4072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2345   -0.1363   -1.7896 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4430   -0.0331   -0.0275 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3794    0.7025    0.9056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6720    0.2046    0.6673 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0772    0.3910    0.1215 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0681   -0.5164    0.4736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3800   -1.7206    0.6592 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3565   -0.1627    0.6466 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9997    0.3308   -0.6246 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4768    0.2944   -0.2055 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3240    0.3257   -1.2826 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5149   -1.0138    0.5578 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1768   -1.2773    1.0076 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9471    0.5686   -2.0215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5048   -1.1287    0.1795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1604    0.5145    1.9627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3277    1.7757    0.6284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6767   -0.7417    0.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8862    1.4181   -0.0496 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4901    0.6600    1.4018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6807    1.3242   -0.9353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8222   -0.4265   -1.4317 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6121    1.1177    0.5169 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1470    0.8339   -1.0138 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2341   -0.9056    1.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8702   -1.8431   -0.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1680   -1.4491    2.0558 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  1  0
  4  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 15 10  1  0
  6 20  1  0
  5 18  1  0
  5 19  1  0
  4 17  1  1
  7 21  1  0
 10 22  1  1
 11 23  1  0
 11 24  1  0
 12 25  1  1
 13 26  1  0
 14 27  1  0
 14 28  1  0
 15 29  1  0
  3 16  1  0
M  END


  Mrv1652304062013452D          

 15 15  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
    0.4875   -0.8277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2020   -0.4152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2269   -0.4152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9806   -0.7507    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5327   -0.1376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1202    0.5769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4557    1.3305    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3132    0.4053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2020   -2.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2020   -2.8902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9165   -3.3027    0.0000 O   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
    1.9165   -0.8277    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6309   -2.0652    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
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0136481

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC(NC(=O)C1CC(O)CN1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H14N2O5/c11-3-6(8(14)15)10-7(13)5-1-4(12)2-9-5/h4-6,9,11-12H,1-3H2,(H,10,13)(H,14,15)

> <INCHI_KEY>
UVSBYUFDCGZIMR-UHFFFAOYSA-N

> <FORMULA>
C8H14N2O5

> <MOLECULAR_WEIGHT>
218.2072

> <EXACT_MASS>
218.090271568

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
20.829224658888073

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-2-[(4-hydroxypyrrolidin-2-yl)formamido]propanoic acid

> <ALOGPS_LOGP>
-3.56

> <JCHEM_LOGP>
-5.300638281614294

> <ALOGPS_LOGS>
-0.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.574867553983417

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3438951848122587

> <JCHEM_PKA_STRONGEST_BASIC>
9.114886597696763

> <JCHEM_POLAR_SURFACE_AREA>
118.89000000000001

> <JCHEM_REFRACTIVITY>
48.2233

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.70e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-2-[(4-hydroxypyrrolidin-2-yl)formamido]propanoic 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       0.910  -1.545   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.244  -0.775   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.424  -0.775   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -1.830  -1.401   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.861  -0.257   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.091   1.077   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.717   2.484   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.585   0.757   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.244  -3.855   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.244  -5.395   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.577  -6.165   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.577  -3.085   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.577  -1.545   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.911  -3.855   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   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
Hydroxyproline serine dipeptide	HMDB
HP-S Dipeptide	HMDB
Hpro-ser	HMDB
HPS Dipeptide	HMDB
Hydroxyproline-serine dipeptide	HMDB
Hydroxyprolylserine	HMDB
L-Hydroxyprolyl-L-serine	HMDB
3-Hydroxy-2-{[hydroxy(4-hydroxypyrrolidin-2-yl)methylidene]amino}propanoate	Generator

Chemical Formula

C₈H₁₄N₂O₅

Average Mass

218.2072 Da

Monoisotopic Mass

218.09027 Da

IUPAC Name

3-hydroxy-2-[(4-hydroxypyrrolidin-2-yl)formamido]propanoic acid

Traditional Name

3-hydroxy-2-[(4-hydroxypyrrolidin-2-yl)formamido]propanoic acid

CAS Registry Number

Not Available

SMILES

OCC(NC(=O)C1CC(O)CN1)C(O)=O

InChI Identifier

InChI=1S/C8H14N2O5/c11-3-6(8(14)15)10-7(13)5-1-4(12)2-9-5/h4-6,9,11-12H,1-3H2,(H,10,13)(H,14,15)

InChI Key

UVSBYUFDCGZIMR-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 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
Proline or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Serine or derivatives
Alpha-amino acid or derivatives
Pyrrolidine carboxylic acid or derivatives
Pyrrolidine-2-carboxamide
Beta-hydroxy acid
Hydroxy acid
Pyrrolidine
1,2-aminoalcohol
Amino acid or derivatives
Amino acid
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Monocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Secondary aliphatic amine
Carboxylic acid
Secondary amine
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Primary alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Amine
Organopnictogen compound
Organic oxygen 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	-3.6	ALOGPS
logP	-5.3	ChemAxon
logS	-0.77	ALOGPS
pKa (Strongest Acidic)	3.34	ChemAxon
pKa (Strongest Basic)	9.11	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	118.89 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	48.22 m³·mol⁻¹	ChemAxon
Polarizability	20.83 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0028872

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

10130637

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Liu KX, Kato Y, Kaku TI, Santa T, Imai K, Yagi A, Ishizu T, Sugiyama Y: Hydroxyprolylserine derivatives JBP923 and JBP485 exhibit the antihepatitis activities after gastrointestinal absorption in rats. J Pharmacol Exp Ther. 2000 Aug;294(2):510-5. [PubMed:10900226 ]

Showing NP-Card for Hydroxyprolyl-Serine (NP0136481)

MOL for NP0136481 (Hydroxyprolyl-Serine)

3D MOL for NP0136481 (Hydroxyprolyl-Serine)

3D SDF for NP0136481 (Hydroxyprolyl-Serine)

3D-SDF for NP0136481 (Hydroxyprolyl-Serine)

PDB for NP0136481 (Hydroxyprolyl-Serine)

3D PDB for NP0136481 (Hydroxyprolyl-Serine)

SMILES for NP0136481 (Hydroxyprolyl-Serine)

INCHI for NP0136481 (Hydroxyprolyl-Serine)

Structure for NP0136481 (Hydroxyprolyl-Serine)

3D Structure for NP0136481 (Hydroxyprolyl-Serine)