Download - SeLnIkRaj - Ligand Scout
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Ligand Scout version 2.02
http://www.inteligand.com/ligandscout/
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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