CADD course learning (2) -- target crystal structure information

CADD Course study （2）-- Target crystal structure information

How to obtain the crystal structure information of the target （PDB）

PDB Database introduction

website ：https://www.rcsb.org/
PDB： Protein crystal structure database （Protein Data Bank）,1971 By the United States Brookhaven、 The establishment of the laboratory , Maintained by the cooperative organization for structural bioinformatics research （RCSB）

PDB The database can be used to obtain the crystal structure and important information of proteins , It is very important to have a reliable protein crystal structure in drug design

PDB Each protein crystal structure in the database has a unique ID, from 0~9 and A-Z A four bit string , Such as Bcr/Abl One of the crystal structures of the target （PDB ID：1lEP）

PDB Data files

With PDB 1IEP For example





Other summaries

HEADER	Molecular class , Publication time , ID
OBSLTE	Indicate this ID No. has been changed to a new one
TITLE	Describe the type of test method
CAVEAT	Possible error messages
COMPND	The molecular composition of the compound
SOURCE	Source of compound
KEYWDS	key word
EXPDTA	The experimental method used to determine the structure
AUTHOR	Structure Tester
REVDAT	Revision date and relevant contents
SPRSDE	Relevant records that have been revoked or changed
JRNL	The publication of coordinate sets
REMARK 1	Relevant literature
REMARK 2	Maximum resolution
REMARK 3	Procedures and statistical methods used
REMARK 4	Other notes
DBREF	Relevant records of other sequence libraries
SEQADVPDB	Discrepancy with other records
MODEL	When there are many subunits, the subunits are displayed
ATOM	Atomic coordinates of the standard group
SIGATM	Standard deviation
ANISOU	Temperature factor
SIGUJ	Standard deviation caused by various temperature factors
TER	End of chain
HETATM	Atomic coordinates of nonstandard groups
ENDMDL	The subunit ends
CONECT	Records about the connectivity between atoms
MASTER	Copyright owner
END	End of file

PDB Database usage

Custom output




Specific crystal complex information download

Look at molecular protein interactions

Some more $\pi$-$\pi$ key ： Mainly face to face and point to point

Select the displayed key ：




practice ：

1. collect Bcr/Abl The protein crystal structure of the target and the small molecule structure involved , Batch download its PDB Structure and organize relevant important information , Such as PDB The resolution of the , Activity value of small ligand , Information of papers corresponding to proteins, etc , Form preliminary targets and their drug molecules （ Including small molecules and antibodies ） Research Report .
2. Collect novel coronavirus Spike Protein and ACE2 Crystal structure of protein , And download its PDB structure , And sort out relevant important information , Such as PDB The resolution of the , Activity value of small ligand , Information of papers corresponding to proteins, etc , Form preliminary targets and their drug molecules （ Including small molecules and antibodies ） Research Report .