TPDB

3D PDB MODEL

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TPDB ID TPDB61487

Peptide_Name

CPP CPP (Penetratin-derived)

Activity

Cell-penetrating Peptides

Activity_category_statistics

Delivery and barrier-penetrating peptides

Database_Source

CPPsite3.0

Sequence_Type

standard

Has_Modification No

Description A 9-aa standard natural cell-penetrating peptides peptide sequence curated from CPPsite3.0, with an available 3D structural model.

Sequence

CKRRMKWKK

FASTA

>TPDB61487|Cell-penetrating Peptides|length=9
CKRRMKWKK

Formula C55H98N20O10S2

Absent Amino Acids ANDEQGHILFPSTYV

Common Amino Acids K

Mass 1263.63

PI 11.63

Basic Residues 6

Acidic Residues 0

Hydrophobic Residues 2

Net Charge +6

Boman Index 3.26

Hydrophobicity -2.344

Aliphatic Index 0.00

Half Life

Mammalian: 1.2 hour Yeast: >20 hour E.coli: >10 hour

Extinction Coefficient Cystines 5500

Absorbance 280nm 435.25

Polar Residues 1

number

0

A

2

R

0

N

0

D

1

C

0

E

0

Q

0

G

0

H

0

I

0

L

4

K

1

M

0

F

0

P

0

S

0

T

1

W

0

Y

0

V

Amino Acid Distribution

A: 0 R: 2 N: 0 D: 0 C: 1 E: 0 Q: 0 G: 0 H: 0 I: 0 L: 0 K: 4 M: 1 F: 0 P: 0 S: 0 T: 0 W: 1 Y: 0 V: 0

Length

9

Formula

C55H98N20O10S2

Mass

1263.63

PI

11.63

Net Charge

+6

Boman Index

3.26

Hydrophobicity

-2.344

C_terminal_Modification

Free

Chirality

L

Ionic_State

Cationic

Linearity

Linear

N_terminal_Modification

Free

SMILES

N[C@@H](CS)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCN=C)C(=O)N[C@@H](CCCN=C)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC1=C(C(=NC1)C)CC)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)O

Evidence 1 Activity

Activity

Detail Source Activity Cell-penetrating Peptides

Target

Cell Line Ht-1080 Cells

Assay & Model

In Vitro Model Female BALB/c nude mice (weighing 18–22 g, 5 wk old)

In Vivo Model Female BALB/c nude mice (weighing 18–22 g, 5 wk old)

Source & Reference

Database Source CPPsite3.0

Source CPPsite3

Other

Source Activity Label	Source Definition
Cell-penetrating Peptides	CPPsite3.0 experimentally validated cell-penetrating peptide annotation.

CPP Category Natural residues Linear L

Source of Peptide Synthetic

Cargo Type FAM-labeled Anti-c-myc siRNA

Subcellular Localization Cytoplasm

Uptake Efficiency Fluorescence intensity was highest for (CPP-siRNA)-NBs (+US) than (CPP-siRNA)-NBs without Ultrasound.

In Vitro or In Vivo In vitro and in vivo

DSSP Secondary Structure CCCCSSCCC

Evidence 2 Activity

Activity

Detail Source Activity Cell-penetrating Peptides

Target

Cell Line MCF-7 Cells

Assay & Model

In Vitro Model MCF-7 tumor-bearing female nude mice

In Vivo Model MCF-7 tumor-bearing female nude mice

Source & Reference

Database Source CPPsite3.0

Source CPPsite3

Other

CPP Category Natural residues Linear L

Source of Peptide Synthetic

Cargo Type FAM-siRNA

Subcellular Localization Cytoplasm

Uptake Efficiency

FAM-siRNA-CPPs/TML (activated) displayed a stronger distribution and higher cellular uptake than FAM-siRNA-CPPs/TML (unactivated).

In Vitro or In Vivo In vitro and in vivo

DSSP Secondary Structure CCCCSSCCC

Evidence 3 Activity

Activity

Detail Source Activity Cell-penetrating Peptides

Target

Cell Line MCF-7 cells

Assay & Model

In Vitro Model MCF-7 tumor-bearing female nude mice

In Vivo Model MCF-7 tumor-bearing female nude mice

Source & Reference

Database Source CPPsite3.0

Source CPPsite3

Other

CPP Category Non-natural residues Linear L Cationic

Source of Peptide Protein derived

Cargo Type Nanocarriers (F-ASPM) containing siRNA-CPPs

Subcellular Localization Cytosol

Uptake Efficiency siRNA-CPPs/F-ASPM (pH 6.5) exhibited the highest mean intensity of 376.27 ± 2.98.

Uptake Mechanism Receptor mediated endocytosis

In Vitro or In Vivo In vitro and in vivo

DSSP_Secondary_Structure

CCCCSSCCC