StarOmics training agenda
Chemicals
Reactions
Enzymes
Pathways
1, StarOmics course,Lausanne, Monday November 19th
Outline
Part I :
• Introduction
• Major chemical classes and functional groups
• Isomery
• Protonation states
• Compound naming
Part II:
• Coding chemical structure
Formula, mol file, SMILES, InChI
• Chemical resources
ChEBI (+classification), KEGG, MetaCyc
ChEMBL, PubChem, etc
Part III:
Chemoinformatics tools: ChemAxon
exercises
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Chemicals
A chemical compound is a pure chemical substance consisting of two or more
different chemical elements.
• Elements (atoms) in a compound are present in a fixed ratio.
Ex: 2 atoms of hydrogen + 1 atom of oxygen becomes 1 molecule of compound-water.
• Atoms are held together in a defined spatial arrangement by chemical bonds.
 Chemical compounds have a unique and defined chemical structure
acetic acid
Formula: C2H4O2
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Identifying compounds
CAS Registry Numbers are unique numerical identifiers assigned by the
Chemical Abstracts Service to every chemical described in the open
scientific literature
The CAS number of acetic acid is 64-19-7
The IUPAC nomenclature of organic chemistry is a
systematic method of naming organic chemical
compounds as recommended by the International Union
of Pure and Applied Chemistry (IUPAC).
Ideally, every possible organic compound should have a
name from which an unambiguous 2D structure can be
created.
Ex: acetic acid is the IUPAC name
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Acetic acid
The IUPAC name is acetic acid.
L-lysine
The IUPAC name is (2S)-2,6-diaminohexanoic acid.
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The IUPAC name is
18-bromo-12-butyl-11-chloro-4,8-diethyl-5-hydroxy-15-methoxytricos-6,13-diene19-yne-3,9-dione.
http://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistry
IUPAC names are rarely used by the biologist community!
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Chemical classes
C: carbon
O: oxygen
S: sulfur
N: nitrogen
P: phosphate
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Functional groups
Functional groups are specific groups of atoms or bonds that
are responsible for the characteristic chemical reactions of
those molecules.
The same functional group will undergo the same or similar
chemical reaction(s) regardless of the size of the molecule it is a
part of. But its relative reactivity can be modified by nearby
functional groups.
Combining the names of functional groups with the names of
the parent alkanes generates a powerful systematic
nomenclature for naming organic compounds.
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Hydrocarbons: common functional groups
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Hydrocarbons: common functional groups
to get more functional groups
 http://en.wikipedia.org/wiki/Functional_group
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Main
functional
groups
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Isomers
same molecular formula
different structural formula
Isomery
Stereoisomers
same atom connectivity
different arrangement in space
Constitutional isomers
different atom connectivities
Enantiomers
mirror images
Z/E or cis/trans
isomers
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Diastereomers
not mirror images
Epimers
Anomers
Others
Enantiomers
• A carbon atom with four different groups is a tetrahedral stereogenic center or
chiral center or asymmetric carbon atom.
• Asymmetric carbons give rise to stereoisomerism.
• A and B are stereoisomers, and more precisely, they are enantiomers.
• In medicinal chemistry and biochemistry, enantiomers are a special concern
because they may possess quite different biological activity.
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Enantiomers / Diastereomers
• Compounds with 2 asymmetric carbons:
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Naming Enantiomers
• Since enantiomers are two different compounds, they need to be
distinguished by name.
• Naming conventions:
 By configuration: R- and SFor chemists, the R / S system is the most important nomenclature
system for denoting enantiomers.
 By optical activity: (+)- and (-) By configuration: D- and L-
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Enantiomers: naming by absolute configuration
R- and S• This system labels each chiral center R or S according to a system by
which its substituents are each assigned a priority, according to the
Cahn-Ingold-Prelog rules (CIP), based on atomic number.
 Examine the atoms directly attached to the stereogenic carbon.
Groups attached with atoms of higher atomic number receive
higher priority, (e.g. O > N > C > H).
 When the attached atoms are identical, move down the next
branching bond of the highest priority, and repeat until a difference
is found, (e.g. -C(CH3)3 > -CH(CH3)2 > -CH2CH3 > -CH3).
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Enantiomers: naming by absolute configuration
R- and S• If the center is oriented so that the lowest-priority of the four is pointed
away from a viewer, the viewer will then see two possibilities:
 If the priority of the remaining three substituents decreases in
clockwise direction, it is labeled R (for Rectus, Latin for right),
 If it decreases in counterclockwise direction, it is S (for Sinister, Latin
for left)
(2S)-2,6-diaminohexanoic acid
(2S,3R)-3-hydroxy-2-methylpentanoic acid
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Enantiomers: naming by optical activity
(+)- and (-)• An enantiomer can be named by the direction in which it rotates the plane of
polarized light.
 If it rotates the light clockwise (as seen by a viewer towards whom the
light is traveling), that enantiomer is labeled (+). Is dextrorotatory.
 Its mirror-image is labeled (−). Is levorotatory.
• Enantiomers are also known as optical isomers due to the fact that two
enantiomers will rotate plane-polarized light in equal, but opposite directions.
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Enantiomers: naming by relative configuration
D- and L• An optical isomer can be named by the spatial configuration of its atoms.
• The D/L system does this by relating the molecule to glyceraldehyde.
Glyceraldehyde has 2 possible configurations labeled D and L (from the Latin
laevus and dexter, meaning left and right, respectively):
• All other molecules are assigned the D- or L- configuration if the chiral center
can be formally obtained from glyceraldehyde by substitution. For this reason
the D- or L- naming scheme is called relative configuration.
• Problem: this naming system can be ambiguous, in contrast to the R/S system.
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Enantiomers: naming by relative configuration
D- and L• Similarity to glyceraldehyde is used to designate configuration
The amino acids in proteins
are exclusively L stereoisomers.
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Enantiomers: naming by relative configuration
D- and L• The D/L system is still very much used for naming sugars.
• When there is more than 1 asymmetric carbon, the D and L are used to relate
configuration of the chiral center most distant from the reducing group (C=O).
 The convention is to arrange the Fischer projection with the carbonyl
group at the top for aldoses and closest to the top for ketoses. The
carbons are numbered from top to bottom.
 If the OH is on the right in the Fischer projection, then it is D
 If the OH is on the left, then it is L
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Enantiomers: relations between the different
system namings
• The R/S system has no fixed relation to the (+)/(-) system. An R isomer can be
either dextrorotatory or levorotatory, depending on its exact ligands.
• The R/S system also has no fixed relation to the D/L system.
• The D/L labeling is unrelated to (+)/(-); it does not indicate which enantiomer is
dextrorotatory and which is levorotatory. Rather, it says that the compound's
stereochemistry is related to that of the dextrorotatory or levorotatory
enantiomer of glyceraldehyde; the dextrorotatory isomer of glyceraldehyde is,
in fact, the D- isomer.
• The D/L system remains in common use in certain areas, such as amino acid
and carbohydrate chemistry. It is convenient to have all of the common amino
acids of higher organisms labeled the same way. In D/L, they are all L. In R/S,
they are not, conversely, all S — most are, but cysteine, for example, is R,
because of sulfur's higher atomic number.
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Alkenes: E/Z (or cis/trans) nomenclature
• The C=C bond cannot rotate and is a most common cause of
diastereomerism.
• When an alkene has more than one substituent, the double bond
geometry is described using the labels E and Z. These labels come from
the German words "entgegen," meaning "opposite," and "zusammen,"
meaning "together."
 Alkenes with the higher priority groups (as determined by CIP rules)
on the same side of the double bond have these groups together
and are designated Z.
 Alkenes with the higher priority groups on opposite sides are
designated E.
• A mnemonic to remember this: Z notation has the higher priority groups
on "ze zame zide."
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Alkenes: E/Z (or cis/trans) nomenclature
(cis)-but-2-ene
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(trans)-but-2-ene
Chemical representation: Fischer projection
• Fischer projections (after the German
chemist Hermann Emil Fischer) is an
ingenious means for representing
configurations of carbon atoms.
• Taking in consideration a carbon center,
place horizontally the bonds extending
towards the observer. The backward bonds
will be vertical. This position is then
shorthanded as two lines: the horizontal
(forward) and the vertical, as showed in the
figure :
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H C
CH2OH
HO
H
CHO
HO C
CH2OH
H
CHO
CHO
CHO
HO
OH
H
OH
CH2OH
CH2OH
CHO
CHO
H
CH2OH
HO
H
CH2OH
Epimers
Epimers : stereoisomers that differ only in configuration about
one chiral center.
H
HO
H
H
CHO
OH
H
OH
OH
CH2OH
D-glucose
HO
HO
H
H
CHO
H
H
OH
OH
CH2OH
D-mannose
epimers
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Anomers and Haworth projection
• Pentoses and hexoses can cyclize in solution.
• The hemiacetal or hemiketal carbon of the cyclic form of carbohydrates is the
anomeric carbon (C1 below).
• Carbohydrate isomers that differ only in the stereochemistry of the anomeric
carbon are called anomers. Anomers are thus epimers at C1.
• The - and -anomers are in equilibrium, and interconvert through the open
form. This process is named mutarotation.
D-glucose
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Isomers of D-arabinose:
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Tautomery
L-ascorbic
acid
CHEBI:29073
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L-xylo-hex-3ulonolactone
CHEBI:28745
Tautomery
spontaneous
L-ascorbic
acid
CHEBI:29073
L-xylo-hex-3ulonolactone
CHEBI:28745
Tautomers are isomers of organic compounds that readily interconvert by a
chemical reaction called tautomerization.
This reaction commonly results in the formal migration of a hydrogen atom or
proton, accompanied by a switch of a single bond and adjacent double bond.
Because of the rapid interconversion, tautomers are generally considered to be the
same chemical compound.
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Acid / Base
Arrhenius: an acid is a substance that dissociates in aqueous solution, releasing a
proton (H+)
dissociation reaction
Ka: dissociation constant
acid-base reaction
Brønsted and Lowry: generalization to a proton exchange reaction
conjugate base
acid
base
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conjugate acid
Dissociation constant
Most molecules contain some specific functional groups likely to lose or gain
proton under specific circumstances.
Each ionization equilibrium between the protonated and deprotonated
forms of the molecule can be described with a constant value called pKa
The dissociation constant Ka is usually written as a quotient of the
equilibrium concentrations (in mol/L), denoted by [HA], [A−] and [H+]:
acid
conjugate base
The logarithmic measure of the acid dissociation constant is more
commonly used in practice:
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Acetic acid
[HA] = [A−] when pH = pKa
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At neutral pH, the major species is acetate ion
acetic acid is conjugate acid of acetate
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L-lysine
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Naming compounds
As the IUPAC name is not commonly used, there are
some issues to reference compounds:
 Same name for different structures
 Different names for same structure
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Compound naming ambiguity
ferulic acid + CoASH + ATP = trans-feruloyl-CoA + products of ATP
breakdown (EC 6.2.1.34)
phenylglyoxylate + NAD+ + CoA-SH = benzoyl-S-CoA + CO2 + NADH
(EC 1.2.1.58)
acyl-CoA + H2O = CoA + a carboxylate
(EC 4.1.1.9)
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Compound naming ambiguity
EC 1.1.1.159
CHEBI:29747
EC 3.1.2.27
 need to use structural data
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Name:cholate
Compounds: coding 2D structure
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Compounds: coding 2D structure
Formula:C6H11O9P
Net charge: -2
• mol file, SDF file
• SMILES,
• InChI
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Molfile / SDF file
• An MDL Molfile is a file format created by MDL (now Symyx
who have merged with Accelrys), for holding information
about the atoms, bonds, connectivity and coordinates of a
molecule.
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Header
Atom block
Bond block
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Charge, repeated unit,…
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Molfile / SDF file
• Molfile format
An MDL Molfile is a file format created by MDL (now Symyx
who have merged with Accelrys), for holding information
about the atoms, bonds, connectivity and coordinates of a
molecule.
• SDF (Structure-Data File) format
SDF files actually wrap the Molfile format.
Multiple compounds are delimited by lines consisting of four
dollar signs ($$$$).
A feature of the SDF format is its ability to include associated
data.
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molecule n-1
molecule n
associated
data
molecule n+1
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SMILES:
Simplified Molecular-Input Line-Entry System
Line notation for describing the structure of chemical molecules
using short ASCII strings.
Generation of SMILES:
Break cycles, then write
as branches off a main
backbone.
http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
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A number of equally valid SMILES can be written for a molecule.
Ex: CCO, OCC and C(O)C all specify the structure of ethanol.
Algorithms have been developed to ensure the same SMILES is generated
for a molecule regardless of the order of atoms in the structure.
 The SMILES is unique for each structure (although dependent on the
canonicalization algorithm used to generate it)
= the Canonical SMILES
isomeric SMILES: string with
information about double bond
configuration and chirality
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InChI: The IUPAC International Chemical Identifier
http://www.iupac.org/inchi/
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Compounds: chemical resources
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Chemical resources: generic resources
 ChEBI
http://www.ebi.ac.uk/chebi/
 MetaCyc
http://metacyc.org/
 KEGG
http://www.genome.jp/kegg/compound/
 ChEMBL
https://www.ebi.ac.uk/chembl/
 PubChem
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound
 ChemProt
http://www.cbs.dtu.dk/services/ChemProt/
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ChEBI – Chemical Entities of Biological Interest
http://www.ebi.ac.uk/chebi/
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ChEBI (Chemical Entities of Biological Interest)
 Non-redundant database of manually annotated chemical
compounds, chemical groups (parts of molecular entities) and
classes of entities
 ChEBI provides a chemical ontology which allows to describe the
relationships between molecular entities or classes of entities
 ChEBI focuses on small molecules, i.e molecules such as nucleic
acids, proteins and peptides derived from proteins by cleavage
are not (will not be) included in ChEBI
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ChEBI (Chemical Entities of Biological Interest)
Each ChEBI 3-stars entity contain:







A unique, unambiguous, recommended ChEBI name and
associated stable unique identifier
A 2D chemical structure when appropriate (small compounds and
groups, but not for classes of compounds)
A definition where appropriate
A collection of synonyms including the IUPAC recommended name
for the entity where appropriate, and brand names and INNs for
drugs
A collection of manually and automatically generated crossreferences to other databases
Links to the ChEBI ontology
Citation information where the chemical has been cited in
publication
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Link to
MarvinView
Applet
Molfile
Additional chemical information
Additional chemical
structures identifiers
Links to the ChEBI ontology
(Structured controlled
vocabulary)
Manually curated
cross-references
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ChEBI classification
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ChEBI classification
L-lysine (CHEBI:18019)
L-lysinate (CHEBI:32550)
L-lysinium(1+) (CHEBI:32551)
D-lysine (CHEBI:16855)
ChEBI ontology
 Janna Hastings, Thursday Nov. 22th
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Searching ChEBI
1. Simple search
 Wild cards available for both Simple
and Advanced search (* character):
 Starting with (Example: aceto*)
 Ending with (Example: *amine)
 Containing (Example: *propyl*)
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Searching ChEBI
2. Advanced search
Structure-based search
Text-based search
Narrow the search by:
 Specific annotation fields
 Compounds sharing common
ontology
 Compounds with specific
chemical properties (formula,
mass/charge
range)
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Searching ChEBI
Example: Searching 3-star compounds with GTP in compound name
Same compound in different
protonation states
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ChEBI download
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Submission to ChEBI
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ChEBI (Chemical Entities of Biological Interest)
ChEBI statistics (Release 96; October 2012)
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MetaCyc compounds
 Curation in MetaCyc covers also chemical compounds.
 Scope: compounds involved in reactions or cofactors
 Compound structures in MetaCyc have been
protonated at pH 7.3 to represent a consistent and
biologically relevant protonation state. Extensive crossreferences to other compound resources (ChEBI, KEGG,
PUBCHEM)
Compounds in MetaCyc organized in an internal class
hierarchy. This allows to define groups of compounds or
navigate and retrieve sets of compounds sharing
functional groups or metabolic purposes
The full list of MetaCyc compounds available at
http://metacyc.org/META/classinstances?object=Compounds
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Stats of MetaCyc V16.1
MetaCyc compounds
MetaCyc compound ontology
(http://metacyc.org/META/class-tree?object=Compounds)
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MetaCyc compounds
Example MetaCyc compound: N-acetyl-β-D-glucosamine
Compound ID
Compound
ontology
Additional
chemical data
Additional chemical
structure identifiers
Cross-references
Reactions/Pathways
including the compounds
Molfile is not directly available
from the public web site
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MetaCyc compounds
Searching MetaCyc compounds
1. Quick Search
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Quick search box (upper right-hand
corner of every MetaCyc page)
MetaCyc compounds
Searching MetaCyc compounds
2. Simple search (compound name/ID)
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3. Advanced search
KEGG compounds
 KEGG LIGAND (http://www.genome.jp/kegg/ligand.html ) is a composite database that
summarizes the knowledge on chemical compounds and reactions stored in KEGG
 KEGG COMPOUND is the
KEGG database of small
molecules, biopolymers and
other entities relevant to
biological systems
 Compounds in KEGG
COMPOUNDS are the basic
building blocks of chemical
reactions stored in KEGG
REACTION
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 KEGG COMPOUNDS stores
extensive cross-reference to
other KEGG databases and
external resources, including
ChEBI
 KEGG COMPOUNDS defined
at fully protonated form
KEGG compounds
Statistics
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KEGG compounds
Example: L-Lysine
Compound ID
Cross-references
KEGG/External
resources
SIMCOMP
search
KEGG REACTIONS
including the
compound
KEGG pathways
including the
compound
EC numbers (Official
IUBMB)associated to
KEGG reactions including
the compound
ChEBI
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cross-references
Cross-References
compound databases
KEGG compounds
Example: L-Lysine
Uncharged compound
This chemical entity
does not exist.
(no pH consideration)
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L-lysine
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KEGG compounds
Searching KEGG COMPOUND
1. Text-based search (Compound ID or
compound name)
http://www.kegg.jp/dbget-bin/www_bfind?compound
2. SIMCOMP/SUBCOMP search: Graph-based
methods to compare chemical structures
http://www.genome.jp/tools/simcomp/
http://www.genome.jp/tools/subcomp/
SIMCOMP (SIMilar COMPounds): Atom-atom
alignments between compound graphs
SUBCOMP (SUBstructure matching of
COMPounds): Common substructure detection
in compound graphs
Input:Compound
ID or Molfile
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KEGG compounds
Example: Search compounds similar to L-lysine (C00043) with SIMCOMP
Map KEGG compounds
to KEGG pathways of
KEGG hierarchies
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ChEBI / KEGG / MetaCyc compounds
http://www.unipathway.org/compound
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Chemical resources: carbohydrates
http://www.science.co.il/biomedical/Carbohydrate-Databases.asp
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Chemical resources: specialized resources
http://www.science.co.il/biomedical/Lipid-Databases.asp
 SystemX.ch: LipidX (http://lipidx.org)
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LipidX
• Insert examples… template => SDF
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ChEBI-izing LipidX
• Insert examples… template => SDF
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ChEBI-izing LipidX
• Insert examples… template => SDF
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Exercises
http://education.expasy.org/cours/StarOmics2012/
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Compound structure analysis: Marvin tools
http://www.chemaxon.com
 Molfiles can be visualized:
 Through MarvinApplet integrated in ChEBI (Limited editing options)
 Though local instalation of Marvin tools (Full editing options)
 Marvin suite is a collection of tools developed by ChemAxon (http://www.chemaxon.com/ ) for
drawing, displaying and analyzing 2D/3D structures of chemical compounds, macromolecules
and reactions
 Calculator Plugins (« Calculations » menu) allow to
calculate physico-chemical properties of chemical
structures:
 Elemental analysis
 Name generator
 Protonation plugins:
 pKa plugin
 Major microspecie plugin
 Isoelectric point pluggin
 2D structures generated locally with Marvin
(Molfiles) can be used as input to the ChEBI
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submission
tool
Compound structure analysis: Marvin tools
Elemental analysis plugin
 Provides basic molecular
values related with the
elemental composition
of the molecule
Naming plugin
 Allows computation of
the IUPAC name or the
Traditional name of any
compound
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Compound structure analysis: Marvin tools
Protonation plugins: pKa (Calculations  Protonation  pKa)
 Calculates the pKa
values of all proton
gaining or losing
atoms on the basis
of the partial charge
distribution
 The chart shows the
microspecies
distribution curves
vs. pH
 The table display the
relative abundance
of different
microspecies across
pH range
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pKa
values
Compound structure analysis: Marvin tools
Protonation plugins: Major
Microspecies (Calculations
 Protonation  Major
Microspecies)
 Determines the major
protonation form at a
specified pH
Protonation plugins:
Isoelectric point
(Calculations  Protonation
 Isoelectric Point)
 Calculates gross
charge distribution
of a molecule as
function of pH.
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