NP-MRD: Showing NP-Card for Pepticinnamin E (NP0332621)

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Record Information

Version

2.0

Created at

2024-03-14 02:45:09 UTC

Updated at

2024-11-01 01:39:05 UTC

NP-MRD ID

NP0332621

Natural Product DOI

https://doi.org/10.57994/1881

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pepticinnamin E

Description

Pepticinnamin E 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. Pepticinnamin E was first documented in 2009 (PMID: 19894725). Based on a literature review a small amount of articles have been published on Pepticinnamin E (PMID: 24059235) (PMID: 32489098) (PMID: 30694017) (PMID: 19890497).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03142402452D          

 65 69  0  0  1  0            999 V2000
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M  END


  Mrv2104 03142402452D          

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M  END
> <DATABASE_ID>
NP0332621

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC\C=C/C1=CC=CC=C1\C=C\C(=O)N[C@H](CC1=CC=C(O)C=C1)C(=O)N(C)[C@@H](CC1=CC=C(OC)C(O)=C1Cl)C(=O)N(C)[C@@H](CC1=CC=CC=C1)C(=O)OC[C@H]1NC(=O)CNC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C49H54ClN5O10/c1-5-6-8-15-33-16-11-12-17-34(33)21-25-42(57)52-37(26-32-18-22-36(56)23-19-32)47(61)54(2)39(28-35-20-24-41(64-4)45(59)44(35)50)48(62)55(3)40(27-31-13-9-7-10-14-31)49(63)65-30-38-46(60)51-29-43(58)53-38/h7-25,37-40,56,59H,5-6,26-30H2,1-4H3,(H,51,60)(H,52,57)(H,53,58)/b15-8-,25-21+/t37-,38-,39+,40+/m1/s1

> <INCHI_KEY>
FAVCPKLIWNVVMG-AGJVLQOFSA-N

> <FORMULA>
C49H54ClN5O10

> <MOLECULAR_WEIGHT>
908.45

> <EXACT_MASS>
907.3559207

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
119

> <JCHEM_AVERAGE_POLARIZABILITY>
93.71461142481095

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R)-3,6-dioxopiperazin-2-yl]methyl (2S)-2-[(2S)-3-(2-chloro-3-hydroxy-4-methoxyphenyl)-2-[(2R)-3-(4-hydroxyphenyl)-N-methyl-2-[(2E)-3-{2-[(1Z)-pent-1-en-1-yl]phenyl}prop-2-enamido]propanamido]-N-methylpropanamido]-3-phenylpropanoate

> <JCHEM_LOGP>
5.770336583333334

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.500675501863618

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.417473520294392

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6687243711015054

> <JCHEM_POLAR_SURFACE_AREA>
203.90999999999997

> <JCHEM_REFRACTIVITY>
246.5465

> <JCHEM_ROTATABLE_BOND_COUNT>
21

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R)-3,6-dioxopiperazin-2-yl]methyl (2S)-2-[(2S)-3-(2-chloro-3-hydroxy-4-methoxyphenyl)-2-[(2R)-3-(4-hydroxyphenyl)-N-methyl-2-[(2E)-3-{2-[(1Z)-pent-1-en-1-yl]phenyl}prop-2-enamido]propanamido]-N-methylpropanamido]-3-phenylpropanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAR-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAR-24         0                                  
HETATM    1  O   UNK     0      -3.573  -3.374   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -1.334  -5.390   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       2.667  -4.620   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   27 Cl   UNK     0       4.001 -10.010   0.000  0.00  0.00          Cl+0
HETATM   28  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       6.668  -5.390   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0      13.337  -3.080   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0      14.670  -2.310   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      16.004  -3.080   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0      16.004  -4.620   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0      14.670  -5.390   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      14.670  -6.930   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      14.670  -0.770   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       0.428  -6.636   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      -9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -13.337  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   53                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   13                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    6                                                       
CONECT   13    4   14   52                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   28                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   26                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   24                                                  
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   21   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   18   27                                                  
CONECT   27   26                                                            
CONECT   28   16   29   51                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   44                                                  
CONECT   32   31   33   43                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36   40                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38   42                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   35   41                                                  
CONECT   41   40                                                            
CONECT   42   37                                                            
CONECT   43   32                                                            
CONECT   44   31   45                                                       
CONECT   45   44   46   50                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   45                                                       
CONECT   51   28                                                            
CONECT   52   13                                                            
CONECT   53    2   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56   60                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   55   61                                                  
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  138    0
END

View in JSmol

Synonyms

Value	Source
Pepticinnamine e	MeSH

Chemical Formula

C₄₉H₅₄ClN₅O₁₀

Average Mass

908.4500 Da

Monoisotopic Mass

907.35592 Da

IUPAC Name

[(2R)-3,6-dioxopiperazin-2-yl]methyl (2S)-2-[(2S)-3-(2-chloro-3-hydroxy-4-methoxyphenyl)-2-[(2R)-3-(4-hydroxyphenyl)-N-methyl-2-[(2E)-3-{2-[(1Z)-pent-1-en-1-yl]phenyl}prop-2-enamido]propanamido]-N-methylpropanamido]-3-phenylpropanoate

Traditional Name

CAS Registry Number

Not Available

SMILES

CCC\C=C/C1=CC=CC=C1\C=C\C(=O)N[C@H](CC1=CC=C(O)C=C1)C(=O)N(C)[C@@H](CC1=CC=C(OC)C(O)=C1Cl)C(=O)N(C)[C@@H](CC1=CC=CC=C1)C(=O)OC[C@H]1NC(=O)CNC1=O

InChI Identifier

InChI=1S/C49H54ClN5O10/c1-5-6-8-15-33-16-11-12-17-34(33)21-25-42(57)52-37(26-32-18-22-36(56)23-19-32)47(61)54(2)39(28-35-20-24-41(64-4)45(59)44(35)50)48(62)55(3)40(27-31-13-9-7-10-14-31)49(63)65-30-38-46(60)51-29-43(58)53-38/h7-25,37-40,56,59H,5-6,26-30H2,1-4H3,(H,51,60)(H,52,57)(H,53,58)/b15-8-,25-21+/t37-,38-,39+,40+/m1/s1

InChI Key

FAVCPKLIWNVVMG-AGJVLQOFSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
mirabilis P8-A2		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
Tyrosine or derivatives
Phenylalanine or derivatives
Alpha-amino acid ester
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Cinnamic acid amide
Cinnamic acid or derivatives
Alpha-amino acid or derivatives
Amphetamine or derivatives
Methoxyphenol
Phenoxy compound
Anisole
Dioxopiperazine
2-halophenol
2-chlorophenol
Methoxybenzene
Phenol ether
Styrene
2,5-dioxopiperazine
Phenol
Chlorobenzene
Alkyl aryl ether
Fatty acid ester
Halobenzene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Fatty acyl
Aryl halide
Benzenoid
Aryl chloride
Piperazine
Monocyclic benzene moiety
1,4-diazinane
Tertiary carboxylic acid amide
Secondary carboxylic acid amide
Lactam
Carboxylic acid ester
Carboxamide group
Ether
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Organooxygen compound
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
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	5.77	ChemAxon
pKa (Strongest Acidic)	8.42	ChemAxon
pKa (Strongest Basic)	-0.67	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	203.91 Å²	ChemAxon
Rotatable Bond Count	21	ChemAxon
Refractivity	246.55 m³·mol⁻¹	ChemAxon
Polarizability	93.71 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

8685394

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10509993

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Moorthy NS, Sousa SF, Ramos MJ, Fernandes PA: Farnesyltransferase inhibitors: a comprehensive review based on quantitative structural analysis. Curr Med Chem. 2013;20(38):4888-923. doi: 10.2174/09298673113206660262. [PubMed:24059235 ]
Ge Y, Wang G, Jin J, Liu T, Ma X, Zhang Z, Geng T, Song J, Ma X, Zhang Y, Yang D, Ma M: Discovery and Biosynthesis of Pepticinnamins G-M Featuring Three Enzymes-Catalyzed Nonproteinogenic Amino Acid Formation. J Org Chem. 2020 Jul 2;85(13):8673-8682. doi: 10.1021/acs.joc.0c01113. Epub 2020 Jun 16. [PubMed:32489098 ]
Santa Maria KC, Chan AN, O'Neill EM, Li B: Targeted Rediscovery and Biosynthesis of the Farnesyl-Transferase Inhibitor Pepticinnamin E. Chembiochem. 2019 Jun 3;20(11):1387-1393. doi: 10.1002/cbic.201900025. Epub 2019 May 2. [PubMed:30694017 ]
Tan KT, Guiu-Rozas E, Bon RS, Guo Z, Delon C, Wetzel S, Arndt S, Alexandrov K, Waldmann H, Goody RS, Wu YW, Blankenfeldt W: Design, synthesis, and characterization of peptide-based rab geranylgeranyl transferase inhibitors. J Med Chem. 2009 Dec 24;52(24):8025-37. doi: 10.1021/jm901117d. [PubMed:19894725 ]
Xu GG, Etzkorn FA: Pin1 as an anticancer drug target. Drug News Perspect. 2009 Sep;22(7):399-407. doi: 10.1358/dnp.2009.22.7.1381751. [PubMed:19890497 ]

Showing NP-Card for Pepticinnamin E (NP0332621)

MOL for NP0332621 (Pepticinnamin E)

3D MOL for NP0332621 (Pepticinnamin E)

3D SDF for NP0332621 (Pepticinnamin E)

3D-SDF for NP0332621 (Pepticinnamin E)

PDB for NP0332621 (Pepticinnamin E)

3D PDB for NP0332621 (Pepticinnamin E)

SMILES for NP0332621 (Pepticinnamin E)

INCHI for NP0332621 (Pepticinnamin E)

Structure for NP0332621 (Pepticinnamin E)

3D Structure for NP0332621 (Pepticinnamin E)