SeLnIkRaj - Ligand Scout

SeLnIkRaJ www.selnikraj.110mb.
com
Ligand Scout version 2.02
http://www.inteligand.com/ligandscout/
Any Queries mail me at selnikraj@yahoo.com

SeLnIkRaJ www.selnikraj.110mb.com
Open Ligand Scout
Taken protein = 1A5W
PDB Id
Type Pdb id and get the protein with the ligand

Place Mouser to check the name of Ligand
Ligand view
Figure 1. The available inhibitor = Y31
Information Bar
Information Regarding
the Ligand Structure
Figure 2. Protein Information updated

Representation molecule by selection Bar
Selection of the Single

Macromolecule from the Ligand
3d
View

In Zoom
2 formats
1, Macromolecule = protein
2, Molecule = Ligand
Expand Of the
Macromolecule and the
Ligand Molecule with the
Option (+), ( - )

Go to Surface Click receptor Binding Pocket
Binding
Pocket
Region
Receptor Binding Pocket
Process Ongoing
Pic showing the Binding pockets

Binding Pockets viewed
The binding Pocket

Region Performed

Ligand Scout Suports on

Hydrogen Bond Donor
Hydrogen Bond Acceptor
Positive Ionizable Area
Negative Ionizable Area
Hydrophobic Interactions
Aromatic Ring
Metal Binding Feature
Excluded Volume
1, Create Pharmacophore
Hydrogen Bond Donor
Alignment Window
Addition of Ligand Molecule to alignment Window
Selected Region Add to Alignment
Add To Alignment

Ligand Molecule in alignment Window
1 Lig Molecule is Added and

Viewed

Menu options in Ligand Scout
These Commands are work out already normal softwares
Go to Edit option and select preference

PDB INTERPREDATION
Chemical feature
Contain Distance ranges Hydrogen Bonding, Metal binding, Hydrobhobicity

Alignment Settings
Maximum Stored Alignments = show how many alignments can add in the alignment
Window,
PREFERENCE of 2D Configuration

Visualization preference
Remote Settings

Ligand Details
1, 2D view of Ligand Details
Information regarding the Y3_1 Ligand Molecule

The Information regarding the Pharmacophore

There are several structures to display the pharmacophores which are present in the
molecule, with the Create Pharmacophore view
The Following picture shows about the description of the representation the structure
view in the Ligand Scout

The position of the Ligand based pharmacophore through the

Step = Create Pharmacophore (MOE)
Hydrogen Bond Acceptor
Excluded Volume
Most of its shows the Hydrogen Bond Acceptors are present of the Most

The Another Protein taken

Taken Protein as 1A5V

Receptor Binding Pocket - option present in the
Surface receptor Binding Pocket Click that
Allignment Window show the parts of @ Ligand

Three Ligands ( 1A5W, 1A5X, 1A5V)
Three Aligned Ligand

Molecules

Three ligands
The Each Ligand Molecule is Colored
1A5V with the Different Colors and then
visualized For the Differentiation Of the
1A5W Ligand Molecule As these Color is
Selected
1A5X
The Aligned Ligand Molecule

with the Selected Colors

Better Alignment View
Taken protein = 1RX2

= 1RB3
Two Different Ligand Molecules In Alignment Window
1RX2 1Rx2 Set as the ref.

Structure
1RB3
Set 1RX2 as Reference Structure and make the Alignment
For Alignment Opt
With ref. 1RX2 the two

Different Ligand are
Selected and Aligned with
reference structure

Scroll Cursor for

the best fit to the
Ligand Molecule
Different View for the

Aligned Ligands

Pharmacophore
for the 1RB3
Left Click that & give

Create Pharmacophore
1RB3 With predicted pharmacophore region
Same Process
Done For the
1RX2
1RX2 with predicted pharmacophore region

The two Ligand

with the predicted
pharmacophores
Two Molecules with predicted Pharmacophore Region
Only
Pharmacophores
viewed
Only pharmacophores view selected

Delete Icon
Selecting the unwanted

Compound
What are the unwanted atoms just select that atom and delete it
Removal of Hyd.atoms
Removal of Hydrogen Atoms
Invisible the Hydrogen Bond atoms

Addition of the Chemical Compound

to the Ligand Molecule
Addition of the Chemical compounds to the Aligned Ligand
Bond Structure
Single double
and triple Bonds
To Change the Bond Single bond to Double and triple bonds

Addition of
Calcium atom
<For Example>
Minimization
Process
Minimization Process

Minimization
Done
Changes
940.380 to
140.3237

SeLnIkRaj - Ligand Scout

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SeLnIkRaJ www.selnikraj.110mb.

Ligand Scout version 2.02

Any Queries mail me at selnikraj@yahoo.com

Open Ligand Scout

Taken protein = 1A5W

Type Pdb id and get the protein with the ligand

Any Queries mail me at selnikraj@yahoo.com

Place Mouser to check the name of Ligand

Figure 1. The available inhibitor = Y31

Figure 2. Protein Information updated

Any Queries mail me at selnikraj@yahoo.com

Representation molecule by selection Bar

Selection of the Single

Any Queries mail me at selnikraj@yahoo.com

Any Queries mail me at selnikraj@yahoo.com

Go to Surface Click receptor Binding Pocket

Receptor Binding Pocket

Pic showing the Binding pockets

The binding Pocket

Any Queries mail me at selnikraj@yahoo.com

Ligand Scout Suports on

Hydrogen Bond Donor

Selected Region Add to Alignment

Any Queries mail me at selnikraj@yahoo.com

Ligand Molecule in alignment Window

1 Lig Molecule is Added and

Any Queries mail me at selnikraj@yahoo.com

Menu options in Ligand Scout

These Commands are work out already normal softwares

Go to Edit option and select preference

Any Queries mail me at selnikraj@yahoo.com

Contain Distance ranges Hydrogen Bonding, Metal binding, Hydrobhobicity

Any Queries mail me at selnikraj@yahoo.com

Any Queries mail me at selnikraj@yahoo.com

Any Queries mail me at selnikraj@yahoo.com

1, 2D view of Ligand Details

Information regarding the Y3_1 Ligand Molecule

Any Queries mail me at selnikraj@yahoo.com

The Information regarding the Pharmacophore

Any Queries mail me at selnikraj@yahoo.com

The position of the Ligand based pharmacophore through the

Hydrogen Bond Acceptor

Any Queries mail me at selnikraj@yahoo.com

The Another Protein taken

Any Queries mail me at selnikraj@yahoo.com

Receptor Binding Pocket - option present in the

Surface receptor Binding Pocket Click that

Allignment Window show the parts of @ Ligand

Three Aligned Ligand

Any Queries mail me at selnikraj@yahoo.com

The Aligned Ligand Molecule

Any Queries mail me at selnikraj@yahoo.com

Better Alignment View

Taken protein = 1RX2

Two Different Ligand Molecules In Alignment Window

1RX2 1Rx2 Set as the ref.

Set 1RX2 as Reference Structure and make the Alignment

For Alignment Opt

With ref. 1RX2 the two

Any Queries mail me at selnikraj@yahoo.com