Peptide

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Cyclo[Ile-Met-Leu-Aile-Pro-Pro-Phe-Phe-D-Val]

Basic information

CPKB ID CP02486
IUPAC Name
(3S,9S,12S,15S,18S,21R,24S,27S,30S)-24,27-dibenzyl-18-[(2S)-butan-2-yl]-9-[(2R)-butan-2-yl]-12-(2-methylpropyl)-15-(2-methylsulfanylethyl)-21-propan-2-yl-1,7,10,13,16,19,22,25,28-nonazatricyclo[28.3.0.03,7]tritriacontane-2,8,11,14,17,20,23,26,29-no
Source

Linum usitatissimum [Division : Plants and Fungi]

Taxonomy :4006 (Viridiplantae-Streptophyta-Malpighiales-Magnoliopsida-Linaceae Linum)  

Wikipedia: Linum usitatissimum

PubChem  

Information

Cyclo[Ile-Met-Leu-aIle-Pro-Pro-Phe-Phe-D-Val] is a natural product found in Linum usitatissimum with data available.

PubChem|163095839  

Legend

Structure

Download structure
2D img
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similarity structure
Molecular Formula

C56H83N9O9S
Molecular Weight 1057.603446 g/mol
SMILES

RUN SEA Predictions

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

PubChem|163095839
InChI
InChI=1S/C56H83N9O9S/c1-10-35(7)46-54(72)57-39(26-29-75-9)48(66)58-40(30-33(3)4)50(68)63-47(36(8)11-2)56(74)65-28-19-25-44(65)55(73)64-27-18-24-43(64)52(70)60-41(31-37-20-14-12-15-21-37)49(67)59-42(32-38-22-16-13-17-23-38)51(69)61-45(34(5)6)53(71)62-46/h12-17,20-23,33-36,39-47H,10-11,18-19,24-32H2,1-9H3,(H,57,72)(H,58,66)(H,59,67)(H,60,70)(H,61,69)(H,62,71)(H,63,68)/t35-,36+,39-,40-,41-,42-,43-,44-,45+,46-,47-/m0/s1  
InChIKey
BRDMGDLQYNAXNM-MDTWGPHWNA-N
2D Structure
PubChem|163095839

Sequence

Graph alignment
Local alignment
IUPAC Condensed
cyclo[Ile-Met-Leu-aIle-Pro-Pro-Phe-Phe-D-Val]  

PubChem|163095839
Amino acid chain
Ile(1)--Met--Leu--aIle--Pro--Pro--Phe--Phe--D-Val(1)  

CyclicPepedia|PP
Graph representation
Ile,Met,Leu,aIle,Pro,Pro,Phe,Phe,D-Val @0,8  

CyclicPepedia|PP
One letter code from Structure
LIPPFFVIM  

CyclicPepedia|Struct2seq
Amino acid chain from Structure
Ile(1)--Pro--Pro--Phe--Phe--Val--Ile--Met--Leu(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|163095839

Chemical and Physical Properties

CyclicPepedia|Struc2Seq + PP

Structure Properties

Property Name Property Value
Exact Mass 1057.603446
Number of Rings 5.0
Complexity 0.493333333
XlogP3 AA 3.4084
Heavy Atom Count 75.0
Hydrogen Bond Donor Count 7.0
Hydrogen Bond Acceptor Count 10.0
Rotatable Bond Count 14.0
Property Name Property Value
Formal Charge 0.0
Refractivity 289.4789
Rule_of_Five 0.0
Number of Atoms 75.0
Topological Polar Surface Area 244.32
Refractivity 289.4789
Veber Rule 0.0
Ghose Filter 0.0
Property Name Property Value
RDKit Fingerprint
01000011101000100100100011011000010000100111010100100010000000101110101111101100100110110010110010000111000001101010011010110010010001001000110001011111100110010100001010000110000110001111100100100100101001001000000000000000010100000101011110001110011100101111000110001000000010001001000000000010011010010010111011000001010100010011111011110110101000000010011001000001000010000000010000000010010100000100000110001100000010000000101000110011111011100000000100010010111000110000000000001010001010110100100000101100110000000100101110010101100110100100100010110110001000000100010010001000000010111100101000110001001010011000100000001001100100101100000110100110001101000110001010100000010101001100011100010010101101100000000100100011011001011000100010001010001110101010001110010000010001110001001010001000011000001000100000001001111010110000010011101101000000110011011100100001000100000100111000001011001101000010111001010110011110011011000001011110101000001000011001010100011000010100001010000001010100000000010000101111011101110011110110001010100000001010010000001000101001100101010001001001110110001001011001010010000000101000000110001001010000000000101000101000101110100110100111001000010010011110000001000000100001001101010111100000011100110111010010010000100101000010001000000000100000110000110001001001011110110000000001101101100001010011111110000001010110110001010010010000100101011000001000000001000001011101000001000111101011001000010011111010001001001011000100000110010000101001110000111011011000000000100100100111000001100000001000010000010110110100010010100000000100100111001001000111100010000001000011000111000000100010110000000100000000000000010000000001010011000100001010000001000000010001011110000100100101000001010111001000100000100011011001010100110010010110100000001000100001010011000001000011111001111100000010110000011110100111110010000000100000000000100011100000010100001101101100000100101101000001010000010101010010000111110110000011011001011011001011100001001001100110000101000000100010000000000001101110000100000000111000000011
Morgan Fingerprint
0100110000110000000100000000000001000000001000000000000000000000100000000000000010000000001000000000000000000100000110000000000000100000000000000000000000000010000000000000000100000000000000000000000000000000000000001000000000000001000000000000000000000100000000000000000000000000000100001001001000000100000000000010000001000000000000010000100000000100000110000000000000000000000000001000010000100000000000000000000000000000000000001001000000000010000000001010000000000000000000000010000000001000000000000001000000000001100000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000010000000000000010001000000000000001000000000100000000000000000000000000000001000100000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000100000000100000000000000001001000000000000000000000000000000000000000000000000000000000000000001000000010000000010000000000000000000001000000000000000000000100000000000001000000000000000000000000010000
MACCS Keys
00000000000000000000000000000000000000000000000000000010000000000000000000100001000101101011110110001000110000110011111011100101110100001110111101111111011110111111110

Sequence Properties

Property Name Property Value
Boman Index -3.01222222222222
Instability 48.4888888888888
Charge -0.00201570060725275
Aliphatic Index 162.222222222222

Manufacturers

Forecasting tools

Information Source

Reference

Pubmed_ID Title DOI Journal

28471681

 Understanding the Diversity and Distribution of Cyclotides from Plants of Varied Genetic Origin 10.1021/acs.jnatprod.7b00061.

J Nat Prod

Understanding the Diversity and Distribution of Cyclotides from Plants of Varied Genetic Origin

Abstract

  • Cyclotides are a large family of naturally occurring plant-derived macrocyclic cystine-knot peptides, with more than 400 having been identified in species from the Violaceae, Rubiaceae, Cucurbitaceae, Fabaceae, and Solanaceae families. Nevertheless, their specialized distribution within the plant kingdom remains poorly understood. In this study, the diversity of cyclotides was explored through the screening of 197 plants belonging to 43 different families. In total, 28 cyclotides were sequenced from 15 plant species, one of which belonged to the Rubiaceae and 14 to the Violaceae. Every Violaceae species screened contained cyclotides, but they were only sparsely represented in Rubiaceae and xistent in other families. The study thus supports the hypothesis that cyclotides are ubiquitous in the Violaceae, and it adds to the list of plants found to express kalata S and cycloviolacin O12. Finally, previous studies suggested the existence of cyclotide isoforms with either an Asn or an Asp at the C-terminal processing site of the cyclotide domain within the precursor proteins. Here we found that despite the discovery of a few cyclotides genuinely containing an Asp in loop 6 as evidenced by gene sequencing, deamidation of Asn during enzymatic digestion resulted in the artifactual presence of Asp isoforms. This result is consistent with studies suggesting that peptides can undergo deamidation after being subjected to external factors, including pH, temperature, and enzymatic digestion.