SMILES

Creating Graphical Objects

Introduction about ACD/ChemSketch

ACD/ChemSketch is a software that make the works of drawing structures of chemical structures of atoms and compounds easier. It consist a lot of useful buttons.

As a basic, we learn to draw chemical bonds (single, double and triple) and atoms using the buttons in the Structure toolbar and general toolbar. For instance, we are being familiarize with Draw Normal tool, Set Bond Vertically button, Undo and Redo buttons, Polymers button and others buttons’ functions. Apart from that, we learn about the cleaning process and also how to flip and make the structures more organized using Clean Structure buttons.

From the basic, we continue to learn how to draw more complex structures using ACD/Chemsketch. We use Table of Radicals to choose the respective structure such as octahydro-1H-indene structure. Furthermore, Markush Bond tools is used to make the selected atom, for example Br, to appear connected to any of the carbon atoms in cyclic structures. ACD/ChemSketch also allows us to generate stereo descriptors for chiral and pseudo chiral centers, and for a double-bond configuration.In addition, using this ACD/ChemSketch, we also can draw the set up of apparatus as required for experiments.

In conclusion, ACD/ChemSketch is a useful software program for students, lecturers, chemists, scientists and everyone who related to chemistry and biology studies for reports and presentations.

Creating Graphical Objects

Energy of Reaction Diagram

p-orbital, d-orbital & pi orbital.

Vacuum Distillation Apparatus

Two chain DNA strand

Lipids & Micelle

Drawing Simple Structures

Bonds, Polymers & Pseudo Atoms

1,3-difluoro-1-(3-phenylpropyl)-5-(8,8,8-trifluorooctyl)cyclononane

Drawing more complex structures

Cation, Anion& Free Radical

Radical Cation, radical anion & triplet radical.

Markush Bond

Markush Bond with Added or Removed Fragment

(2Z)-4-chloropent-2-ene, (2E)-4-chloropent-2-ene & 1,4-dimethylcyclohexane with Stereo Descriptors

{1-(methoxy-κO)-2-[2-(methoxy-κO)ethoxy-κO]ethane}(phenyl)lithium

Delocalized Charges and Curves

2-methyl-1-[2-(phenyldiazenyl)phenyl]butan-2-ol, spatial arrangement of atoms, delocalization of double bonds, tautomeric or aromatic structure & organometallic complex

3-D Macromolecule

[Side 1]

Primary Citation
Crystal structure of LexA: a conformational switch for regulation of self-cleavage.

Authors: Luo Y, Pfuetzner RA, Mosimann S, Paetzel M, Frey EA, Cherney M, Kim B, Little JW, Strynadka NC.

Journal: (2001) Cell(Cambridge,Mass.) 106: 585-594

PubMed: 11551506

PubMed Abstract:

LexA repressor undergoes a self-cleavage reaction. In vivo, this reaction requires an activated form of RecA, but it occurs spontaneously in vitro at high pH. Accordingly, LexA must both allow self-cleavage and yet prevent this reaction in the absence of... [ Read More & Search PubMed Abstracts ]

LexA repressor undergoes a self-cleavage reaction. In vivo, this reaction requires an activated form of RecA, but it occurs spontaneously in vitro at high pH. Accordingly, LexA must both allow self-cleavage and yet prevent this reaction in the absence of a stimulus. We have solved the crystal structures of several mutant forms of LexA. Strikingly, two distinct conformations are observed, one compatible with cleavage, and the other in which the cleavage site is approximately 20 A from the catalytic center. Our analysis provides insight into the structural and energetic features that modulate the interconversion between these two forms and hence the rate of the self-cleavage reaction. We suggest RecA activates the self-cleavage of LexA and related proteins through selective stabilization of the cleavable conformation.

Related Structures:
Primary Citation of: 1JHC 1JHE 1JHF 1JHH Also Cited By: 1Z0L

Organizational Affiliation:
Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada.

[Side 2]

Molecular Description

Classification : Hydrolase
Structure Weight : 29848.40
Molecule : LEXA REPRESSOR
Polymer : 1
Type : Polypeptide (L)
Length : 135 residues
Chains : A, B
EC Number : 3.4.21.88
Fragment : C-Terminus, Residues 68-202
Mutation : L89P, Q92W, E152A, K156A


Source

Polymer : 1
Scientific name : Escherichia coli
Expression System : Escherichia coli

[Side 3]

Experimental Details

Method: X-RAY DIFFRACTION
Experimental Data: [ EDS ]

Resolution[Å]:	2.50
R-Value:	0.220 (work)
R-Free:	0.284
Space Group:	C 2

Unit Cell:
	Length [Å]	Angles [°]
	a = 124.70	α = 90.00
	b = 43.70	β = 109.50
	c = 49.50	γ = 90.00

-------------------------------------------------

Related PDB Enteries

Id	Details
1JHC	LEXA S119A C-terminal tryptic fragment
1JHF	LEXA G85D MUTANT
1JHH	LEXA S119A MUTANT

Derived Data

• SCOP Classification v1.75 - (2 Domains)
• CATH Classification v3.3.0 - (2 Domains)
• PFAM Classification - (2 Domains)
• GO Terms - (10 Terms)

Source : RCSB PDB
3-D molecules can be viewed using RasWin software.

Journey of Life

Time : 1440
Place : Orkid Comp. Lab

KOS 1110. The code of the subject which I am doing my assignment now. The task is to create a blogspot and to post an entry entitles "Journey of Life", just like this entry's title. The task must to be completed in 3 hours period. I thought it is just a simple task, however, many of my classmates having problems. So, I'll post a picture of this class later.

Btw, let me briefing you about the last entry's picture (as if anyone want to read that!).Yesterday, I planned with At to have lunch near the lake in front of Mahallah Maimunah. So, A responsibled to spread a messege to our other 6 friends, Z, S, F, Aq, W, S. The funny things was, they really thought that we would have 'the real picnic' near the lake. Meaning, picnic with mattress and food! That was contrast with my imagination, only to have a luch at the gazebo! That's it.

Task : had to post an image.

The compound between Biological Science building, Kuliyyah of Sciences (left) and Kuliyyah of Dentistry(right).
Sorry, but this is NOT picture taken by me.

Sorry...I'll post the picture of the class -taken with At phone- later.

Time Editted Done :1523