This document discusses identifying the active site of an enzyme. It begins by introducing the concepts of binding sites and how they relate to drug design. The active site is described as being a three-dimensional cleft formed by amino acid groups, taking up a small part of the enzyme's volume. Features of active sites include being clefts or crevices that bind substrates via weak attractions in a precisely defined arrangement. The document outlines steps for active site identification, including analyzing the protein structure to find the binding pocket and key interaction sites. It also discusses classifying ligand and protein atoms and characterizing the reconstructed binding pocket.

1. Lecture 6 –Active site identification
BTT- 516– Drug Designing and Development

2. •Introduction
•Feature of the active site
•Structure
•Binding site
•Models for active site of enzyme
•Properties thatAffect Binding
•Mechanism of catalytic site
Topics to be covered

3. Introduction
• In biochemistry, a binding site is a region on a
protein or piece of DNA or RNA to which ligands
(specific molecules and/or ions) may form a
chemical bond. An equilibrium exists between
unbound ligands and bound ligands
• In dug design it is the site in the receptor/ protein
at which the drug binds
• The ligand receptor binding is very important in
deciding ligands fate as a drug
•Active sites of enzyme is that point where,
substrate bind for the chemical reaction.
•Active site generally found on the surface of
enzyme and in some enzyme it is a “Pit” like structure
Or
Active site

4. Feature of the active site
▶The active site is a three-dimensional cleft formed by groups
that come from different parts of the amino acid sequence
▶The active site takes up a relatively small part of the total
volume of an enzyme
▶ Active sites are clefts or crevices
▶ Substrates are bound to enzymes by multiple weak attractions.
▶The specificity of binding depends on the precisely defined
arrangement of atoms in an active site.

5. Active site identification is the first step
• It analyzes the protein to find the binding pocket, derives key interaction sites
within the binding pocket, and then prepares the necessary data for Ligand
fragment link.
• The basic inputs for this step are the 3Dstructure of the protein and a pre-
docked ligand in PDB format, as well as their atomic properties.
Lock and key theory Induced fit model

6. Both ligand and protein atoms need to be classified and their
atomic properties should be defined, basically, into four
atomic types:
• Hydrophobic atom: All carbons in hydrocarbon chains or in
aromatic groups.
• H-bond donor: Oxygen and nitrogen atoms bonded to hydrogen
atom(s).
• H-bond acceptor: Oxygen and sp2 or sp hybridized nitrogen
atoms with lone electron pair(s).
• Polar atom: Oxygen and nitrogen atoms that are neither H-bond
donor nor H-bond acceptor, sulfur, phosphorus, halogen, metal,
and carbon atoms bonded to hetero-atom(s).

7. Characterization of the binding pocket

8. Not every ligand atom contacts a protein atom and thus leaves space
between parts of the ligand and the protein. The space is partially
occupied by crystallographic observable water molecules. The
reconstructed pocket shape shown as a black coloured mesh, the ligand
shown in various colour and the oxygen atoms of the water molecules
shown as green coloured spheres.

9. Thank you
Er. Rajan Rolta
Faculty of Applied Sciences and Biotechnology
Shoolini University,
Village Bhajol, Solan (H.P)
+91-7018792621 (Mob No.)
rajanrolta@shooliniuniversity.com