PDB

PROTEIN DATA BANK

INTRODUCTION

• The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.
• These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans.
• Obtain by X-ray crystallography (80%) or NMR spectroscopy (16%)
• Submitted by biologists and biochemists from around the world.

For more information visit: Protein Data Bank

AMYLASE 

Classification	Alpha Amylase
Structure Weight	48016.77
Molecule	ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE
Type	Protein
Length	425

TRYPSIN

Classification	Complex (proteinase/inhibitor)
Structure Weight	29892.08
Molecule	BETA-TRYPSIN
Type	Protein
Length	223

PEPSIN 

Classification	Hydrolase (acid Proteinase)
Structure Weight	34469.8
Molecule	PEPSIN
Type	Protein
Length	326

HTRA

Classification	Protein Binding
Structure Weight	14890.9
Molecule	Putative serine protease
Type	Protein
Length	134

CARBOXYPEPTIDASE

Classification	Carboxypeptidase
Structure Weight	138865.59
Molecule	CARBOXYPEPTIDASE A
Type	Protein
Length	307

smiles :)

Simplified Molecular Input Line

Entry Specifications

INTRODUCTION OF SMILES

• SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings.

• SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

LAW OF SMILE

1) SMILES Bonds  

SINGLE*                    -

DOUBLE                    =

TRIPLE                      #

AROMATIC*              :

2) SMILES Branches

• Represented by enclosure in parentheses
• Can be nested or stacked
• Examples:    

               1) OCC(C)C is iso-Butanol
                    2) OC(C)(C)C is tert-Butanol

3) SMILES Conventions

• Avoid two consecutive left parentheses if possible
• Strive for the fewest number of possible branches
• Tautomeric bonds are not designated; enter the appropriate form

SMILES notation by using ChemSketch. :)

SMILES	Name	SMILES	Name
CC	ETHANE	[OH3+]	HYDRONIUM ION
C#N	HYDROGEN CYANIDE	[235U]	URANIUM-235
O=C=O	CARBON DIOXIDE	[2H]O[2H]	DEUTREIUM OXIDE

Click the link below for
1. SMILECAS Database Files

2. SMILES Tutorial