SeLnIkRaj - Ligand Scout

8/14/2019 SeLnIkRaj - Ligand Scout

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SeLnIkRaJ www.selnikraj.110mb.com

Ligand Scout version 2.02

http://www.inteligand.com/ligandscout/

Any Queries mail me at [email protected]
http://www.inteligand.com/ligandscout/http://www.inteligand.com/ligandscout/


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Open Ligand Scout

Taken protein = 1A5W

PDB Id

Type Pdb id and get the protein with the ligand



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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



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Representation molecule by selection Bar

Selection of the Single

Macromolecule from the Ligand

3d

View



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In Zoom

2 formats1, Macromolecule = protein

2, Molecule = Ligand

Expand Of theMacromolecule and the

Ligand Molecule with theOption (+), ( - )



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Go to Surface Click receptor Binding Pocket

Binding

PocketRegion

Receptor Binding Pocket

Process Ongoing

Pic showing the Binding pockets

Binding Pockets viewed

The binding Pocket

Re ion Performed



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Ligand Scout Suports on

Hydrogen Bond Donor

Hydrogen Bond Acceptor

Positive Ionizable AreaNegative Ionizable Area

Hydrophobic InteractionsAromatic RingMetal Binding Feature

Excluded Volume

1, Create Pharmacophore

Hydrogen Bond Donor

Alignment WindowAddition of Ligand Molecule to alignment Window

Selected Region Add to Alignment

Add To Alignment



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Ligand Molecule in alignment Window

1 Lig Molecule is Added andViewed



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Menu options in Ligand Scout

These Commands are work out already normal softwares

Go to Edit option and select preference



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PDB INTERPREDATION

Chemical feature

Contain Distance ranges Hydrogen Bonding, Metal binding, Hydrobhobicity



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Alignment Settings

Maximum Stored Alignments = show how many alignments can add in the alignment

Window,

PREFERENCE of 2D Configuration



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Visualization preference

Remote Settings



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Ligand Details

1, 2D view of Ligand Details

Information regarding the Y3_1 Ligand Molecule



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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



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The position of the Ligand based pharmacophore through theStep = Create Pharmacophore (MOE)

Hydrogen Bond Acceptor

Excluded Volume

Most of its shows the Hydrogen Bond Acceptors are present of the Most



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The Another Protein takenTaken Protein as 1A5V



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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 LigandMolecules



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Three ligands

The Each Ligand Molecule is Colored

with the Different Colors and thenvisualized For the Differentiation Of the

Ligand Molecule As these Color is

Selected

1A5V

1A5W

1A5X

The Aligned Ligand Molecule

with the Selected Colors



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Better Alignment View

Taken protein = 1RX2

= 1RB3

Two Different Ligand Molecules In Alignment Window

1RB3

1Rx2 Set as the ref.

Structure1RX2

Set 1RX2 as Reference Structure and make the Alignment

For Alignment Opt

With ref. 1RX2 the two

Different Ligand are

Selected and Aligned withreference structure



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Scroll Cursor for

the best fit to the

Ligand Molecule

Different View for theAli ned Li ands



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Left Click that & giveCreate Pharmaco hore

Pharmacophorefor the 1RB3

1RB3 With predicted pharmacophore region

Same Process

Done For the

1RX2

1RX2 with predicted pharmacophore region



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The two Ligand

with the predicted

pharmacophores

Two Molecules with predicted Pharmacophore Region

Only

Pharmacophores

viewed

Only pharmacophores view selected



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Delete Icon

Selecting the unwantedCom ound

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



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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



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Addition of

Calcium atom

Minimization

Process

Minimization Process



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Minimization

Done

Changes940.380 to

140.3237

Documents

SeLnIkRaj - Ligand Scout