BIOMD0000000169
type: SBMLModel
name: Mass_Action_2
parameter: metaid_0000014
is version of: GO:0031575
parameter: metaid_0000008
parameter: metaid_0000018
reaction: metaid_0000055
species: metaid_0000042
reaction: metaid_0000073
is: MODEL3897395081
species: metaid_0000041
function def: metaid_0000005
species: metaid_0000039
reaction: metaid_0000061
parameter: metaid_0000025
parameter: metaid_0000035
substance units: metaid_0000003
notes: The model reproduces the time profiles of p27, E2F and aE/cdk2 as depicted in Figure 5 c of the paper. Model was simulated on MathSBML. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
parameter: metaid_0000033
reaction: metaid_0000076
occurs in: http://identifiers.org/taxonomy/40674
function def: metaid_0000003
name: Mass_Action_0
parameter: metaid_0000012
parameter: metaid_0000022
reaction: metaid_0000072
reaction: metaid_0000063
reaction: metaid_0000059
parameter: metaid_0000028
reaction: metaid_0000053
species: metaid_0000048
compartment: metaid_0000038
parameter: metaid_0000020
parameter: metaid_0000030
reaction: metaid_0000069
curated: true
name: Aguda1999_CellCycle
species: metaid_0000045
parameter: metaid_0000015
parameter: metaid_0000009
parameter: metaid_0000019
reaction: metaid_0000056
reaction: metaid_0000066
name: Mass_Action_1
time units: metaid_0000027
parameter: metaid_0000006
parameter: metaid_0000036
species: metaid_0000040
is described by: http://identifiers.org/pubmed/10619492
species: metaid_0000047
parameter: metaid_0000013
parameter: metaid_0000023
parameter: metaid_0000029
area units: metaid_0000005
reaction: metaid_0000064
parameter: metaid_0000021
parameter: metaid_0000031
reaction: metaid_0000074
length unit: length
parameter: metaid_0000010
reaction: metaid_0000070
reaction: metaid_0000060
parameter: metaid_0000016
parameter: metaid_0000026
reaction: metaid_0000051
volume units: metaid_0000004
reaction: metaid_0000057
reaction: metaid_0000067
species: metaid_0000044
species: metaid_0000043
parameter: metaid_0000007
parameter: metaid_0000037
function def: metaid_0000004
reaction: metaid_0000054
reaction: metaid_0000050
parameter: metaid_0000024
parameter: metaid_0000034
reaction: metaid_0000065
parameter: metaid_0000032
reaction: metaid_0000075

metaid_0000014
type: Parameter
constant: true
value: 0.016
name: kminus4

metaid_0000008
type: Parameter
constant: true
value: 0.1
name: k1

metaid_0000018
type: Parameter
constant: true
value: 5.0
name: kminus6

metaid_0000055
type: Reaction
kinetic law: 710726
product: 710714
fast: false
reversible: false
name: E2F synthesis

710714
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000040

metaid_0000040
type: Species
is version of: IPR015633
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000038
name: E2F

metaid_0000038
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

metaid_0000042
type: Species
has version: P24941
initial concentration: NaN
in compartment: metaid_0000038
is version of: P24864
boundary condition: false
initial amount: 0.01
is version of: P24941
has only substance units: true
constant: false
has version: O96020
name: i_cyclinE_CDK2

metaid_0000073
type: Reaction
kinetic law: 711303
modifier: 711291
product: 711279
fast: false
reversible: false
name: pRB synthesis inhibited by p16

metaid_0000048
type: Species
is homolog to: P42771
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 5.0
in compartment: metaid_0000038
name: p16

711279
type: SpeciesReference
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species: metaid_0000044

metaid_0000044
type: Species
is version of: IPR015652
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.05
in compartment: metaid_0000038
name: pRB

metaid_0000041
type: Species
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initial concentration: NaN
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boundary condition: false
is version of: C00562
is version of: IPR015652
has only substance units: true
constant: false
name: pRB_P

metaid_0000039
type: Species
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initial concentration: NaN
has only substance units: true
name: pRB_E2F
constant: false
has part: IPR015633
initial amount: 1.95
in compartment: metaid_0000038
boundary condition: false

metaid_0000061
type: Reaction
kinetic law: 710883
modifier: 710871
reactant: 710859
fast: false
reversible: false
name: p27 degradation via cycE/CDK2

metaid_0000043
type: Species
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has version: P24864
has version: P24941
initial concentration: NaN
in compartment: metaid_0000038
initial amount: 0.0
constant: false
boundary condition: false
name: a_cyclinE_CDK2
has only substance units: true

710859
type: SpeciesReference
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species: metaid_0000046

metaid_0000046
type: Species
is homolog to: P46527
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 15.0
in compartment: metaid_0000038
name: p27

metaid_0000025
type: Parameter
constant: true
value: 0.05
name: k19

metaid_0000035
type: Parameter
constant: true
value: 0.01
name: k27

metaid_0000033
type: Parameter
constant: true
value: 0.01
name: k26

metaid_0000076
type: Reaction
kinetic law: 711387
product: 711375
reactant: 711363
fast: false
reversible: false
name: pRB-p dephosphorylation

711375
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000044

711363
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

metaid_0000012
type: Parameter
constant: true
value: 0.0
name: k3p

metaid_0000022
type: Parameter
constant: true
value: 0.035
name: K10

metaid_0000072
type: Reaction
kinetic law: 711267
modifier: 711255
product: 711243
fast: false
reversible: false
name: p16 synthesis inhibited by pRB

711243
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000048

metaid_0000063
type: Reaction
kinetic law: 710979
product: 710967
product: 710955
reactant: 710943
fast: false
reversible: false
name: cycE/CDK2/p27 deassociation

710967
type: SpeciesReference
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species: metaid_0000046

710955
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

710943
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000047

metaid_0000047
type: Species
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name: cycE_CDK2_p27
boundary condition: false
constant: false
has version: P24864
has version: P24941
in compartment: metaid_0000038
has only substance units: true
initial concentration: NaN
initial amount: 1.0
has version: P46527

metaid_0000059
type: Reaction
kinetic law: 710822
reactant: 710810
fast: false
reversible: false
name: cycD/CDK4 degradation

710810
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000045

metaid_0000045
type: Species
has version: P11802
boundary condition: false
initial amount: 0.0
has only substance units: true
initial concentration: NaN
in compartment: metaid_0000038
name: CycD_CDK4
has version: IPR015451
constant: false

metaid_0000028
type: Parameter
constant: true
value: 0.001
name: k22

metaid_0000053
type: Reaction
kinetic law: 710666
product: 710654
reactant: 710642
fast: false
reversible: false
name: cycE/CDK2 deactivation

710654
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

710642
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

metaid_0000020
type: Parameter
constant: true
value: 2.0
name: k8

metaid_0000030
type: Parameter
constant: true
value: 0.1
name: k24

metaid_0000069
type: Reaction
kinetic law: 711183
reactant: 711171
fast: false
reversible: false
name: p27 degradation

711171
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000046

metaid_0000015
type: Parameter
constant: true
value: 0.001
name: kminus1

metaid_0000009
type: Parameter
constant: true
value: 0.1
name: k2

metaid_0000019
type: Parameter
constant: true
value: 1.0E-5
name: k7

metaid_0000056
type: Reaction
kinetic law: 710750
reactant: 710738
fast: false
reversible: false
name: E2F degradation

710738
type: SpeciesReference
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species: metaid_0000040

metaid_0000066
type: Reaction
kinetic law: 711087
product: 711075
reactant: 711063
reactant: 711051
fast: false
reversible: false
name: cycD/CDK4/p27 complex formation

711075
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000049

metaid_0000049
type: Species
has version: IPR015451
has only substance units: true
has version: P11802
has version: P46527
in compartment: metaid_0000038
initial amount: 0.0
name: cycD_CDK4_p27
constant: false
boundary condition: false
initial concentration: NaN

711063
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000045

711051
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000046

metaid_0000006
type: Parameter
constant: true
value: 0.5
name: k1p

metaid_0000036
type: Parameter
constant: true
value: 0.01
name: k28

metaid_0000013
type: Parameter
constant: true
value: 1.0E-6
name: k4

metaid_0000023
type: Parameter
constant: true
value: 3.5
name: k17

metaid_0000029
type: Parameter
constant: true
value: 0.2
name: k23

metaid_0000064
type: Reaction
kinetic law: 711015
reactant: 711003
reactant: 710991
fast: false
reversible: false
name: cycD/CDK4/p16 complex formation

711003
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000048

710991
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000045

metaid_0000021
type: Parameter
constant: true
value: 2.0
name: k9

metaid_0000031
type: Parameter
constant: true
value: 0.01
name: k25

metaid_0000074
type: Reaction
kinetic law: 711327
product: 711315
fast: false
reversible: false
name: pRB synthesis

711315
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000044

metaid_0000010
type: Parameter
constant: true
value: 1.0
name: kminus2

metaid_0000070
type: Reaction
kinetic law: 711207
product: 711195
fast: false
reversible: false
name: p16 synthesis

711195
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000048

metaid_0000060
type: Reaction
kinetic law: 710847
product: 710835
fast: false
reversible: false
name: p27 synthesis

710835
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000046

metaid_0000016
type: Parameter
constant: true
value: 0.02
name: k5

metaid_0000026
type: Parameter
constant: true
value: 0.01
name: k20

metaid_0000051
type: Reaction
kinetic law: 710594
product: 710582
reactant: 710570
reactant: 710558
fast: false
reversible: false
name: pRB/E2F complex formation

710582
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000039

710570
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000040

710558
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000044

metaid_0000057
type: Reaction
kinetic law: 710774
reactant: 710762
fast: false
reversible: false
name: icycE/CDK2 degradation

710762
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

metaid_0000067
type: Reaction
kinetic law: 711135
product: 711123
product: 711111
reactant: 711099
fast: false
reversible: false
name: cycD/CDK4/p27 complex deassociation

711123
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000045

711111
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000046

711099
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000049

metaid_0000007
type: Parameter
constant: true
value: 0.5
name: k1pp

metaid_0000037
type: Parameter
constant: true
value: 0.001
name: k29

metaid_0000054
type: Reaction
kinetic law: 710702
modifier: 710690
product: 710678
fast: false
reversible: false
name: icycE/CDK2 synthesis

710678
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

metaid_0000050
type: Reaction
name: pRB/E2F complex deassociation
product: 710474
reversible: false
fast: false
product: 710486
modifier: 710498
kinetic law: 710546
modifier: 710510
reactant: 710462
modifier: 710522
modifier: 710534

710474
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000040

710486
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

710462
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000039

metaid_0000024
type: Parameter
constant: true
value: 1.0E-5
name: k18

metaid_0000034
type: Parameter
constant: true
value: 0.1
name: k26p

metaid_0000065
type: Reaction
kinetic law: 711039
product: 711027
fast: false
reversible: false
name: E2F auto stimulation

711027
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000040

metaid_0000032
type: Parameter
constant: true
value: 0.02
name: k25p

metaid_0000075
type: Reaction
kinetic law: 711351
reactant: 711339
fast: false
reversible: false
name: pRB degradation

711339
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000044

metaid_0000011
type: Parameter
constant: true
value: 1.42
name: k3

metaid_0000071
type: Reaction
kinetic law: 711231
reactant: 711219
fast: false
reversible: false
name: p16 degradation

711219
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000048

metaid_0000017
type: Parameter
constant: true
value: 0.018
name: k6

metaid_0000027
type: Parameter
constant: true
value: 0.1
name: k21

metaid_0000058
type: Reaction
kinetic law: 710798
product: 710786
fast: false
reversible: false
name: cycD/CDK4 synthesis

710786
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000045

metaid_0000052
type: Reaction
kinetic law: 710630
product: 710618
reactant: 710606
fast: false
reversible: false
name: cycE/CDK2 activation

710618
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

710606
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

metaid_0000062
type: Reaction
kinetic law: 710931
product: 710919
reactant: 710907
reactant: 710895
fast: false
reversible: false
name: cycE/CDK2/p27 complex formation

710919
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000047

710907
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000046

710895
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

metaid_0000068
type: Reaction
kinetic law: 711159
reactant: 711147
fast: false
reversible: false
name: acycE/CDK2 degradation

711147
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

W3 CDTF: Thu Jul 05 15:42:01 BST 2012

W3 CDTF: Thu Apr 03 14:23:34 BST 2008

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri