<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="1">
<model id="Binding_inhibition">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
This is an example of competetive binding.  IkB binds to active form of NFkB to form a complex.  IKK phosphorylates IkB, and the phosphorylated IkB is ubiquinated automatically, and degraded.  The phosphorylated form of IkB can not bind to NFkB.  Therefore, IkB is an inhibitor of NFkB, while IKK decreases the amount of unphosphorylated IkB, thus prevent it from binding NFkB.
</body>
</html>
</notes>
<annotation>
<celldesigner:modelVersion>0.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
<celldesigner:listOfIncludedSpecies>
<celldesigner:species id="s7" name="NF_kappa_B">
<celldesigner:annotation>
<celldesigner:complexSpecies>s5</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p44</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s6" name="I_kappa_B">
<celldesigner:annotation>
<celldesigner:complexSpecies>s5</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p43</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
<celldesigner:listOfCompartmentAliases>
</celldesigner:listOfCompartmentAliases>
<celldesigner:listOfComplexSpeciesAliases>
<celldesigner:complexSpeciesAlias id="csa1" species="s5">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="430.0" y="221.72680755925484" w="71.0" h="65.92868024562335"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="71.0" height="65.92868024562335"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:complexSpeciesAlias>
</celldesigner:listOfComplexSpeciesAliases>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>active</celldesigner:activity>
<celldesigner:bounds x="246.5" y="55.65548780487819" w="50.0" h="25.0"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="-1246.0" y="183.5"/>
<celldesigner:boxSize width="50.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2" species="s2">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="191.5" y="156.1554878048782" w="50.0" h="25.0"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="-1326.0" y="287.0"/>
<celldesigner:boxSize width="50.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa3" species="s3">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="311.5" y="155.6554878048782" w="50.0" h="25.0"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="-1206.0" y="286.5"/>
<celldesigner:boxSize width="50.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa4" species="s4">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="193.0" y="239.8445121951218" w="50.0" h="25.0"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="-1324.5" y="370.6890243902436"/>
<celldesigner:boxSize width="50.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa5" species="s8">
<celldesigner:activity>active</celldesigner:activity>
<celldesigner:bounds x="306.5" y="287.1554878048782" w="50.0" h="25.0"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="-1206.0" y="433.0"/>
<celldesigner:boxSize width="50.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa6" species="s9">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="203.0" y="313.3445121951218" w="30.0" h="30.0"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="-1314.5" y="444.1890243902436"/>
<celldesigner:boxSize width="30.0" height="30.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffcccc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa7" species="s6" complexSpeciesAlias="csa1">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="445.0" y="231.6554878048782" w="50.0" h="25.0"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="15.0" y="9.928680245623354"/>
<celldesigner:boxSize width="50.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="0.0" height="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa8" species="s7" complexSpeciesAlias="csa1">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="444.50000000000045" y="256.6554878048782" w="50.0" h="25.0"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="14.500000000000455" y="34.928680245623354"/>
<celldesigner:boxSize width="50.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="0.0" height="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
<celldesigner:protein id="p42" name="IKK" type="GENERIC"/>
<celldesigner:protein id="p44" name="NF_kappa_B" type="GENERIC"/>
<celldesigner:protein id="p43" name="I_kappa_B" type="GENERIC">
<celldesigner:listOfModificationResidues>
<celldesigner:modificationResidue angle="3.141592653589793" id="rs1" name="" side="none"/>
<celldesigner:modificationResidue angle="1.9265354949219762" id="rs2" name="" side="none"/>
</celldesigner:listOfModificationResidues>
</celldesigner:protein>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfBlockDiagrams/>
</annotation>
<listOfCompartments>
<compartment id="default"/>
</listOfCompartments>
<listOfSpecies>
<species id="s1" name="IKK" compartment="default" initialAmount="0">
<annotation>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p42</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re1"/>
</celldesigner:listOfCatalyzedReactions>
</annotation>
</species>
<species id="s5" name="Complex_br_(I_kappa_B/NF_kappa_B)" compartment="default" initialAmount="0">
<annotation>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>Complex_br_(I_kappa_B/NF_kappa_B)</celldesigner:name>
</celldesigner:speciesIdentity>
</annotation>
</species>
<species id="s8" name="NF_kappa_B" compartment="default" initialAmount="0">
<annotation>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p44</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</annotation>
</species>
<species id="s9" name="a127_degraded" compartment="default" initialAmount="0">
<annotation>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>DEGRADED</celldesigner:class>
<celldesigner:name>a127_degraded</celldesigner:name>
</celldesigner:speciesIdentity>
</annotation>
</species>
<species id="s2" name="I_kappa_B" compartment="default" initialAmount="0">
<annotation>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p43</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
<celldesigner:modification residue="rs1" state="phosphorylated"/>
</celldesigner:listOfModifications>
</celldesigner:state>
</celldesigner:speciesIdentity>
</annotation>
</species>
<species id="s3" name="I_kappa_B" compartment="default" initialAmount="0">
<annotation>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p43</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</annotation>
</species>
<species id="s4" name="I_kappa_B" compartment="default" initialAmount="0">
<annotation>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p43</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
<celldesigner:modification residue="rs1" state="phosphorylated"/>
<celldesigner:modification residue="rs2" state="ubiquitinated"/>
</celldesigner:listOfModifications>
</celldesigner:state>
</celldesigner:speciesIdentity>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" reversible="false" fast="false">
<annotation>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s3" alias="sa3"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s2" alias="sa2"/>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
<celldesigner:lineDirection index="2" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.3333333333333339,0.0 0.666666666666667,-8.881784197001252E-16</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="CATALYSIS" modifiers="s1" aliases="sa1" targetLineIndex="-1,1">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</annotation>
<listOfReactants>
<speciesReference species="s3">
<annotation>
<celldesigner:alias>sa3</celldesigner:alias>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2">
<annotation>
<celldesigner:alias>sa2</celldesigner:alias>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="s1">
<annotation>
<celldesigner:alias>sa1</celldesigner:alias>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
<reaction id="re2" reversible="false" fast="false">
<annotation>
<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s3" alias="sa3"/>
<celldesigner:baseReactant species="s8" alias="sa5"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s5" alias="csa1"/>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints num0="0" num1="0" num2="0">0.37535319738994755,0.3119209854949414</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
</annotation>
<listOfReactants>
<speciesReference species="s3">
<annotation>
<celldesigner:alias>sa3</celldesigner:alias>
</annotation>
</speciesReference>
<speciesReference species="s8">
<annotation>
<celldesigner:alias>sa5</celldesigner:alias>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s5">
<annotation>
<celldesigner:alias>csa1</celldesigner:alias>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
<reaction id="re3" reversible="false" fast="false">
<annotation>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s2" alias="sa2"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s4" alias="sa4"/>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
<celldesigner:lineDirection index="2" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.3333333333333339,0.0 0.666666666666667,-1.7763568394002505E-15</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
</annotation>
<listOfReactants>
<speciesReference species="s2">
<annotation>
<celldesigner:alias>sa2</celldesigner:alias>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s4">
<annotation>
<celldesigner:alias>sa4</celldesigner:alias>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
<reaction id="re4" reversible="false" fast="false">
<annotation>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s4" alias="sa4"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s9" alias="sa6"/>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
<celldesigner:lineDirection index="2" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.3333333333333339,0.0 0.6666666666666679,0.0</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
</annotation>
<listOfReactants>
<speciesReference species="s4">
<annotation>
<celldesigner:alias>sa4</celldesigner:alias>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s9">
<annotation>
<celldesigner:alias>sa6</celldesigner:alias>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
