NP-MRD: Showing NP-Card for Cyclo-(Phe-Ser) (NP0332001)

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Record Information

Version

2.0

Created at

2023-10-18 12:00:20 UTC

Updated at

2025-02-11 15:45:17 UTC

NP-MRD ID

NP0332001

Natural Product DOI

https://doi.org/10.57994/1122

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cyclo-(Phe-Ser)

Description

Cyclo-(Phe-Ser) belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Cyclo-(Phe-Ser) was first documented in 2023 (PMID: 37794774). Based on a literature review a small amount of articles have been published on Cyclo-(Phe-Ser).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10182312002D          

 17 18  0  0  0  0            999 V2000
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
  4 16  1  0  0  0  0
 16 17  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332001

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1NC(=O)C(CC2=CC=CC=C2)NC1=O

> <INCHI_IDENTIFIER>
InChI=1/C12H14N2O3/c15-7-10-12(17)13-9(11(16)14-10)6-8-4-2-1-3-5-8/h1-5,9-10,15H,6-7H2,(H,13,17)(H,14,16)

> <INCHI_KEY>
WIJKWEYCUNYTGY-UHFFFAOYNA-N

> <FORMULA>
C12H14N2O3

> <MOLECULAR_WEIGHT>
234.255

> <EXACT_MASS>
234.100442319

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
22.86204640772073

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-benzyl-6-(hydroxymethyl)piperazine-2,5-dione

> <JCHEM_LOGP>
-0.46362159366666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.738028669314229

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.689749827042014

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8443995994143467

> <JCHEM_POLAR_SURFACE_AREA>
78.43

> <JCHEM_REFRACTIVITY>
60.757500000000014

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-benzyl-6-(hydroxymethyl)piperazine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 18-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-OCT-23         0                                  
HETATM    1  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       5.335  -3.080   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       2.667  -4.620   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   16                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    2   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16                                                       
CONECT   16   15    4   17                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₄N₂O₃

Average Mass

234.2550 Da

Monoisotopic Mass

234.10044 Da

IUPAC Name

3-benzyl-6-(hydroxymethyl)piperazine-2,5-dione

Traditional Name

3-benzyl-6-(hydroxymethyl)piperazine-2,5-dione

CAS Registry Number

Not Available

SMILES

OCC1NC(=O)C(CC2=CC=CC=C2)NC1=O

InChI Identifier

InChI=1/C12H14N2O3/c15-7-10-12(17)13-9(11(16)14-10)6-8-4-2-1-3-5-8/h1-5,9-10,15H,6-7H2,(H,13,17)(H,14,16)

InChI Key

WIJKWEYCUNYTGY-UHFFFAOYNA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600, C2D6OS, simulated)	[email protected]	Tianjin University of Traditional Chinese Medicine	zhanglihua	2024-05-09	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Paraconiothyrium sp. YK-03		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Dioxopiperazine
2,5-dioxopiperazine
Monocyclic benzene moiety
1,4-diazinane
Piperazine
Benzenoid
Carboxamide group
Lactam
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organic oxide
Organopnictogen compound
Alcohol
Carbonyl group
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-0.46	ChemAxon
pKa (Strongest Acidic)	10.69	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	78.43 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	60.76 m³·mol⁻¹	ChemAxon
Polarizability	22.86 Å³	ChemAxon
Number of Rings	2	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

Not Available

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gao WK, Song XY, Li SW, Xue BX, Wu HH, Zhang LH, Pei YH: A rare tetrahydroimidazopyridine from the marine-derived fungus Paraconiothyrium sp. YK-03. Nat Prod Res. 2023 Oct 5:1-7. doi: 10.1080/14786419.2023.2262720. [PubMed:37794774 ]
DOI: 10.1080/14786419.2023.2262720

Showing NP-Card for Cyclo-(Phe-Ser) (NP0332001)

MOL for NP0332001 (Cyclo-(Phe-Ser))

3D MOL for NP0332001 (Cyclo-(Phe-Ser))

3D SDF for NP0332001 (Cyclo-(Phe-Ser))

3D-SDF for NP0332001 (Cyclo-(Phe-Ser))

PDB for NP0332001 (Cyclo-(Phe-Ser))

3D PDB for NP0332001 (Cyclo-(Phe-Ser))

SMILES for NP0332001 (Cyclo-(Phe-Ser))

INCHI for NP0332001 (Cyclo-(Phe-Ser))

Structure for NP0332001 (Cyclo-(Phe-Ser))

3D Structure for NP0332001 (Cyclo-(Phe-Ser))