Peptide

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Drymarin B

Basic information

CPKB ID CP01739
IUPAC Name
(3S,6S,9S,15S,21S)-6-benzyl-3-[(4-hydroxyphenyl)methyl]-15-(2-methylpropyl)-1,4,7,13,16,19-hexazatricyclo[19.3.0.09,13]tetracosane-2,5,8,14,17,20-hexone
Source

Drymaria cordata [Division : Plants and Fungi]

Taxonomy :191453 (Viridiplantae-Streptophyta-Caryophyllales-Magnoliopsida-Caryophyllaceae Drymaria)  

Wikipedia: Drymaria cordata

PubChem  

Family

Orbitide   Cybase  

Information

Drymarin B is a natural product found in Drymaria cordata with data available.

PubChem|101044251   Cybase|685  

Legend

Structure

Download structure
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similarity structure
Molecular Formula

C36H46N6O7
Molecular Weight 674.3427978 g/mol
SMILES

RUN SEA Predictions

 CC(C)C[C@@H]1NC(=O)CNC(=O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccc(O)cc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C1=O  

PubChem|101044251
InChI
InChI=1S/C36H46N6O7/c1-22(2)18-27-35(48)42-17-7-11-30(42)34(47)39-26(19-23-8-4-3-5-9-23)32(45)40-28(20-24-12-14-25(43)15-13-24)36(49)41-16-6-10-29(41)33(46)37-21-31(44)38-27/h3-5,8-9,12-15,22,26-30,43H,6-7,10-11,16-21H2,1-2H3,(H,37,46)(H,38,44)(H,39,47)(H,40,45)/t26-,27-,28-,29-,30-/m0/s1  
InChIKey
QAPRFGWSSPGDPK-QUTGOYNDNA-N
2D Structure
PubChem|101044251
3D Structure
PubChem|101044251

Sequence

Graph alignment
Local alignment
One-letter code

PFYPGL

Cybase|685
IUPAC Condensed
cyclo[Gly-Leu-Pro-Phe-Tyr-Pro]  

PubChem|101044251
Amino acid chain
Gly(1)--Leu--Pro--Phe--Tyr--Pro(1)  

CyclicPepedia|PP
Graph representation
Gly,Leu,Pro,Phe,Tyr,Pro @0,5  

CyclicPepedia|PP
One letter code from Structure
LPFYPG  

CyclicPepedia|Struct2seq
Amino acid chain from Structure
Leu(1)--Pro--Phe--Tyr--Pro--Gly(1)  

CyclicPepedia|Struct2seq
Description of the conversion sequence The one letter code and Amino acid chain derived from the structural transformation may be inconsistent, with the Amino acid chain containing Essential Amino acid and the one letter code not.
svg Image

PubChem|101044251

Chemical and Physical Properties

CyclicPepedia|PP

Structure Properties

Property Name Property Value
Exact Mass 674.3427978
Number of Rings 5.0
Complexity 0.673469388
XlogP3 AA 0.7897
Heavy Atom Count 49.0
Hydrogen Bond Donor Count 5.0
Hydrogen Bond Acceptor Count 7.0
Rotatable Bond Count 6.0
Property Name Property Value
Formal Charge 0.0
Refractivity 179.6836
Rule_of_Five 0.0
Number of Atoms 49.0
Topological Polar Surface Area 177.25
Refractivity 179.6836
Veber Rule 0.0
Ghose Filter 0.0
Property Name Property Value
RDKit Fingerprint
01000010101000100100100011011000010000100111010000101010000000100010101111101000100110010010110010000111000001001010001000110010000001001000110000001111100110000100001010100110100110011111100100100100101001001000000000000000010100000101001110001100011100101111000110001000000010001001100000000010011010010010101001000001010100000010111011010110101000000010011000000001000010000000000000000010010100000100000110001100000010000000101000110011110011100000000100010110111000010000000000000010001010010100100000101100110000000100101110010101100110000100100010010110001000000100010010001000000010111000101000110001101010011000100000001001100100110100000010100110000001000110001010100000000101011100011100010010100101100000000100100011001001011000100010001010001110101010001110010010000001100001001010001000001000001000100000001001111010110000010011101001010000110010011101100001010100000100111000000011001101000010111000010100011110011010000000011110001000001010011101010000011000010100001010000001010100000000000000101101001101110011110110001010100000001010000000001010101001100001000001001001110110000001001101010010000000101000000110001001010000000000101000001000100110100110100111001000010010011110000001000000000001001101010011100000011100110111000010010000100101000010001000100000000000110000110001001001011010100001000001100010100001000011111110000001010110110001010000010000000101011000001000000101100001001100000001000101100011001000000011111110001101001011000100000110010000100001110000111011011001000000100100100111000001100000001000010000010110100100000010100000000110100111001001010101100010000001000010000001000000100010110000000100000000100000010000000001000011000100101010000101000010000001011110000100100101000001010110001000100000100011011001010100010010010110100000000000100001010010000000000011111001101100000010110000011110100111110011000000100000000000100011100000010000001101101100000100101101000001010000010101010010000111110110000001011001011011001000000011001001100110000001000000100010010000000001101110000100000000111000000011
Morgan Fingerprint
0100110000100000000100000000100001000000001000000000000000000000100000000000000010000000001000000000000000000000000100000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000000000001000000100000000000000000000000000000000000000000000100001100000000000100000000100010000000000000000000010000100000000000000010000000000000000000000000000000010000000000000000000000000000000000000000001001000010000010000000001010000000000000000000000000000000000000000000010001000000000000000000000000000000000000000000010000000000000000000000000010000000000000000000000000000000000000000000000000000000100000000000000010000000000000010000000000000000001000000000100000000000000000000000000000001000100000000000000100000000100000000000000000000000000000000000000000000000000001000100000000000100000000000000000010000001001000000000000000000000000000000000000000000100000000000000000000000000000010000000010000000000000000001001000000000000000000000000000000000000000001000000000000000000010000
MACCS Keys
00000000000000000000000000000000000000000000000000000010000000000000000000100001001101000011100110001000110000110101011011100101110110001111101101111111111111111111110

Sequence Properties

Property Name Property Value
Boman Index -1.45
Instability 115.333333333333
Charge -0.00286611482556564
Aliphatic Index 64.9999999999999

Manufacturers

Manufacturers Name Value
CreativePeptides
Bayer healthcare pharmaceuticals
Upsher smith laboratories
Merck
Manufacturers Name Value
Apotex
Baxter Healthcare Corp
Pharmasources
Novartis
AstraZeneca

Forecasting tools

Information Source

Property Name Property ID
Patents QAPRFGWSSPGDPK-QUTGOYNDNA-N
pubchem 101044251
Drugbank
DRAMP3
Uniprot
Cybase 685
CONOSERVER
BindingDB
CHEMBL CHEMBL3425644
CTD
Wikipedia
KEGG Compound/Drug
CHEBI QAPRFGWSSPGDPK-QUTGOYNDNA-N
EPA DSSTox
FDA Global Substance Registration System (GSRS)
DTP/NCI
Chemspider QAPRFGWSSPGDPK-QUTGOYNDNA-N

Reference

Pubmed_ID Title DOI Journal

16621155

 Antimicrobial peptides from diverse families isolated from the skin of the Asian frog, Rana grahami 10.1016/j.peptides.2006.03.002.

Peptides

Antimicrobial peptides from diverse families isolated from the skin of the Asian frog, Rana grahami

Abstract

  • Seven peptides with antimicrobial activity were isolated in pure form from an extract of the skin of the Yunnanfu Kunming frog Rana grahami Boulenger, 1917. The peptides were identified as belonging to the nigrocin-2 (three peptides), brevinin-1 (one peptide), brevinin-2 (three peptides), and esculentin-1 (one peptide) families. Nigrocin-2GRb (GLFGKILGVGKKVLCGLSGMC) containing three lysine residues, represented the peptide with highest potency against microorganisms (MIC = 3 microM against Escherichia coli, 12.5 microM against Staphylococcus aureus and 50 microM against Candida albicans) and the greatest hemolytic activity against human erythrocytes (LD50 = 40 microM). In contrast, nigrocin-2GRa (GLLSGILGAGKHIVCGLSGLC) and nigrocin-2GRc (GLLSGILGAGKNIVCGLSGLC), with only a single lysine residue, showed weak antimicrobial and hemolytic activity. Phylogenetic relationships among Eurasian ranid frogs are less well understood than those of North American ranids but the primary structures of the R. grahami antimicrobial peptides suggest a close relationship of this species with the Japanese pond frogs R. nigromaculata and R. porosa brevipoda.