CADD course learning (3) -- target drug interaction

CADD Course study （3）-- Target drug interactions

PyMol Software tutorial

Basic operation

Rotate the image arbitrarily ： Aim at any part of the image, click the left mouse button, and then move the mouse
Zoom in / Zoom out the image ： Aim at any part of the image, click the right mouse button, and then move the mouse （ Up is shrinking , Down is zoom ）
Move the image ： Aim at any part of the image and click the middle mouse button or scroll wheel , Then move the mouse command line to enter ：fetch 1lEP

from PDB Download crystal structure from database website 1lEP, stay pymol open

• Step1： Change interface color （Display One Background-White）
• Step2： Deletion protein B chain , Enter at the command line ‘remove chainB’, press return
• Step3： Remove ions and water molecules （14.75 and 129 Water molecules interact with ligands , So keep ）： Select chloride ion and corresponding water molecule in the column of sequence information , Action object sele
  （Action-remove atoms）
  
  Step4： Show cartoon shapes （Action-present-ligand sites-cartoon）
  Step5： Copy to obj01（Action-copy to object-new
  
  Step6： Action object 1iep, Now it only shows cartoons （Hide-sticks&Hide-lines）
  
  Step7： Action object obj01, Now it only shows ligands and amino acids （Hide-cartoon）
  

Step8： Click the object with the mouse 1iep, Don't show cartoon temporarily ; Right click on the operation interface , Select... From the pop-up box center（vis）, Make objects obj01 centered
Step9： Action object 1iep_pol_conts. Change the color of hydrogen bond （Color-reds-red）

The green stick shows imatinib , Surrounded by interacting amino acids , The red ball is a water molecule , To better see the interactions , Need further operation
Step10： Select the amino acids with hydrogen bonds around the ligand , Displayed as a stick （Show-sticks;Label-residues）
Step11： Action object obj01, Hide the rest of the amino acids （Hide-Lines）

The display size of water molecules can be set ：
（Setting-Edit All, Call up the setting box , take nb_spheres_size The size of is changed to 0.4, press return ） Select the amino acids around the ligand , Unified display color , operation sele object ：
（Color-by element Choose the fifth color here ）

As you can see from the picture ：

1. The nitrogen atom on the pyridine ring of the compound is related to M318 The ammonia formed hydrogen bonds , The nitrogen atom on the piperazine ring of the compound is related to I360 and H361 Form hydrogen bond , The two imino nitrogen atoms of the compound are also related to E286 and T315 Form hydrogen bond
2. K271,E286,H361 and D381 It also interacts with compounds indirectly through water bridges

How to get a beautiful combination pattern diagram ？
3. There is no main chain or side chain involved in the interaction in the hidden amino acid ： Selected amino acids , Action object sele（Hide-main chain or side chain;Hide-label）
4. Action object liep, Change the cartoon style （Color-blues-lightblue）
5. Adjust the angle of the mouse , Enable clear display of target drug interactions

setting-cartoon-smooth-loops

We adjusted the angle to clearly observe the target drug interaction , How to export pictures ？

1. Set parameters ray_shadows by 0 （Setting-Edit All, Call up the setting box , take ray_shadows The size of is changed to 0, press return ）
2. Life today line input ：ray 1600,1200
3. Then you can export the pictures （File-Save lmage As-PNG; The amino acid number can be found in photoshop add to ）