NP-MRD: Showing NP-Card for cyclo(L-Pro-L-Phe) (NP0351473)

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Record Information

Version

2.0

Created at

2025-08-21 02:47:45 UTC

Updated at

2025-08-21 04:00:44 UTC

NP-MRD ID

NP0351473

Natural Product DOI

https://doi.org/10.57994/4520

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cyclo(L-Pro-L-Phe)

Description

Cyclo(L-Pro-L-Phe), also known as cyclo(L-phe-L-pro), 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(L-Pro-L-Phe) was first documented in 2017 (PMID: 28632179). Based on a literature review a significant number of articles have been published on cyclo(L-Pro-L-Phe) (PMID: 31623138) (PMID: 31184497) (PMID: 40778764) (PMID: 37914258) (PMID: 37360689) (PMID: 33387853).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02242319582D          

 19 21  0  0  1  0            999 V2000
    3.2789    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    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
  4  3  1  0  0  0  0
  4  5  1  1  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
 12  2  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
 12 16  1  6  0  0  0
 12 17  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
  4 18  1  0  0  0  0
 18 19  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0351473

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CCCN1C(=O)[C@H](CC1=CC=CC=C1)NC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H16N2O2/c17-13-12-7-4-8-16(12)14(18)11(15-13)9-10-5-2-1-3-6-10/h1-3,5-6,11-12H,4,7-9H2,(H,15,17)/t11-,12-/m0/s1

> <INCHI_KEY>
QZBUWPVZSXDWSB-RYUDHWBXSA-N

> <FORMULA>
C14H16N2O2

> <MOLECULAR_WEIGHT>
244.294

> <EXACT_MASS>
244.121177763

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
24.787051476146253

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,8aS)-3-benzyl-octahydropyrrolo[1,2-a]pyrazine-1,4-dione

> <JCHEM_LOGP>
0.8559539506666669

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.236835589976323

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.28093034444007

> <JCHEM_PKA_STRONGEST_BASIC>
-4.04293089413071

> <JCHEM_POLAR_SURFACE_AREA>
49.410000000000004

> <JCHEM_REFRACTIVITY>
66.90290000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
cyclo(L-phe-L-pro)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-23         0                                  
HETATM    1  O   UNK     0       6.121   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       7.454   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.788  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.788  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.122  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.122  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.788  -5.390   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.454  -4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.454  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0       6.121   0.770   0.000  0.00  0.00           H+0
HETATM   17  N   UNK     0       4.787   0.000   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   18                                                  
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   16   17                                             
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   17                                                       
CONECT   16   12                                                            
CONECT   17   12   15   18                                                  
CONECT   18   17    4   19                                                  
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Value	Source
(3S-trans)-3-Benzylhexahydropyrrolo(1,2-a)pyrazine-1,4-dione	Kegg
Cyclo(L-phe-L-pro)	MeSH

Chemical Formula

C₁₄H₁₆N₂O₂

Average Mass

244.2940 Da

Monoisotopic Mass

244.12118 Da

IUPAC Name

(3S,8aS)-3-benzyl-octahydropyrrolo[1,2-a]pyrazine-1,4-dione

Traditional Name

cyclo(L-phe-L-pro)

CAS Registry Number

Not Available

SMILES

[H][C@@]12CCCN1C(=O)[C@H](CC1=CC=CC=C1)NC2=O

InChI Identifier

InChI=1S/C14H16N2O2/c17-13-12-7-4-8-16(12)14(18)11(15-13)9-10-5-2-1-3-6-10/h1-3,5-6,11-12H,4,7-9H2,(H,15,17)/t11-,12-/m0/s1

InChI Key

QZBUWPVZSXDWSB-RYUDHWBXSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 850 MHz, CDCl3, experimental)	jseyun12@gmail.com	School of Pharmacy, Sungkyunkwan University	Se Yun Jeong	2025-08-21	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces sp. M45		Not Available

Chemical Taxonomy

Description

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
N-alkylpiperazine
Monocyclic benzene moiety
1,4-diazinane
Piperazine
Benzenoid
Pyrrolidine
Tertiary carboxylic acid amide
Carboxamide group
Lactam
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic molecular entity (CHEBI:69440 )

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	0.86	ChemAxon
pKa (Strongest Acidic)	11.28	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	49.41 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	66.9 m³·mol⁻¹	ChemAxon
Polarizability	24.79 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

C00038889

Chemspider ID

Not Available

KEGG Compound ID

C11847

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443440

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Shaala LA, Youssef DTA, Badr JM, Harakeh SM, Genta-Jouve G: Bioactive Diketopiperazines and Nucleoside Derivatives from a Sponge-Derived Streptomyces Species. Mar Drugs. 2019 Oct 16;17(10). pii: md17100584. doi: 10.3390/md17100584. [PubMed:31623138 ]
Xiang WX, Liu Q, Li XM, Lu CH, Shen YM: Four pairs of proline-containing cyclic dipeptides from Nocardiopsis sp. HT88, an endophytic bacterium of Mallotus nudiflorus L. Nat Prod Res. 2020 Aug;34(15):2219-2224. doi: 10.1080/14786419.2019.1577834. Epub 2019 Jun 11. [PubMed:31184497 ]
Jeong SY, He MT, Kim M, Nam KH, Poulsen M, Beemelmanns C, Kang KS, Kim KH: Anti-adipogenic effects of N-acetyltyramine from termite-associated Streptomyces sp. M45. Org Biomol Chem. 2025 Aug 8. doi: 10.1039/d5ob01062d. [PubMed:40778764 ]
Ishizu T, Fujitani Y, Nishio R, Kamei H: Chiral Recognition of Diketopiperazine Containing Proline Residues by (-)-Epigallocatechin-3-O-gallate in Water. Chem Pharm Bull (Tokyo). 2023;71(11):804-811. doi: 10.1248/cpb.c23-00369. [PubMed:37914258 ]
Li L, Xu Z, Cao R, Li J, Wu CJ, Wang Y, Zhu H: Effects of hydroxyl group in cyclo(Pro-Tyr)-like cyclic dipeptides on their anti-QS activity and self-assembly. iScience. 2023 Jun 7;26(7):107048. doi: 10.1016/j.isci.2023.107048. eCollection 2023 Jul 21. [PubMed:37360689 ]
Gonzalez-Lopez O, Palacios-Nava BB, Pena-Uribe CA, Campos-Garcia J, Lopez-Bucio J, Garcia-Pineda E, Reyes de la Cruz H: Growth promotion in Arabidopsis thaliana by bacterial cyclodipeptides involves the TOR/S6K pathway activation. J Plant Physiol. 2021 Feb;257:153343. doi: 10.1016/j.jplph.2020.153343. Epub 2020 Dec 15. [PubMed:33387853 ]
Carrieri R, Borriello G, Piccirillo G, Lahoz E, Sorrentino R, Cermola M, Bolletti Censi S, Grauso L, Mangoni A, Vinale F: Antibiotic Activity of a Paraphaeosphaeria sporulosa-Produced Diketopiperazine against Salmonella enterica. J Fungi (Basel). 2020 Jun 10;6(2):83. doi: 10.3390/jof6020083. [PubMed:32531985 ]
Zhu H, Sun SW, Li H, Chang A, Liu YC, Qian J, Shen YL: Significantly improved production of Welan gum by Sphingomonas sp. WG through a novel quorum-sensing-interfering dipeptide cyclo(L-Pro-L-Phe). Int J Biol Macromol. 2019 Apr 1;126:118-122. doi: 10.1016/j.ijbiomac.2018.12.189. Epub 2018 Dec 22. [PubMed:30583004 ]
Song S, Fu S, Sun X, Li P, Wu J, Dong T, He F, Deng Y: Identification of Cyclic Dipeptides from Escherichia coli as New Antimicrobial Agents against Ralstonia Solanacearum. Molecules. 2018 Jan 19;23(1):214. doi: 10.3390/molecules23010214. [PubMed:29351264 ]
Hernandez-Padilla L, Vazquez-Rivera D, Sanchez-Briones LA, Diaz-Perez AL, Moreno-Rodriguez J, Moreno-Eutimio MA, Meza-Carmen V, Cruz HR, Campos-Garcia J: The Antiproliferative Effect of Cyclodipeptides from Pseudomonas aeruginosa PAO1 on HeLa Cells Involves Inhibition of Phosphorylation of Akt and S6k Kinases. Molecules. 2017 Jun 20;22(6):1024. doi: 10.3390/molecules22061024. [PubMed:28632179 ]
DOI: 10.1039/d5ob01062d
PMID: 40778764

Showing NP-Card for cyclo(L-Pro-L-Phe) (NP0351473)

MOL for NP0351473 (cyclo(L-Pro-L-Phe))

3D MOL for NP0351473 (cyclo(L-Pro-L-Phe))

3D SDF for NP0351473 (cyclo(L-Pro-L-Phe))

3D-SDF for NP0351473 (cyclo(L-Pro-L-Phe))

PDB for NP0351473 (cyclo(L-Pro-L-Phe))

3D PDB for NP0351473 (cyclo(L-Pro-L-Phe))

SMILES for NP0351473 (cyclo(L-Pro-L-Phe))

INCHI for NP0351473 (cyclo(L-Pro-L-Phe))

Structure for NP0351473 (cyclo(L-Pro-L-Phe))

3D Structure for NP0351473 (cyclo(L-Pro-L-Phe))