478265
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000025
reversible: false
is: GO:0030693
fast: false
product: 478349
is: http://identifiers.org/ec-code/3.4.22.56
product: 478336
reactant: 478324
name: Caspase 9 cleavage by cleaved caspase 3 when Apaf-1 is bound
reactant: 478312
type: Reaction
kinetic law: 478361

metaid_0000015
in compartment: metaid_0000086
boundary condition: false
name: APAF-1-Caspase 9 cleaved complex
has part: P55211
initial amount: NaN
type: Species
constant: false
initial concentration: 0.0
has only substance units: false
has part: O14727

metaid_0000042
kinetic law: 478946
reactant: 478933
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 9 cleaved degradation
type: Reaction

metaid_0000062
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

477879
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

478013
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

478651
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000043
kinetic law: 478970
reactant: 478958
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1 Caspase 9 cleaved degradation
type: Reaction

477916
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000024
is: GO:0030693
reactant: 478265
fast: false
kinetic law: 478300
name: Caspase 9 cleavage by cleaved caspase 3
product: 478288
reactant: 478253
type: Reaction
is: http://identifiers.org/ec-code/3.4.22.56
product: 478276
reversible: false

metaid_0000014
is version of: P55211
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000086
name: Caspase 9 cleaved
type: Species

metaid_0000080
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478958
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

477964
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000063
constant: true
units: metaid_0000089
value: 0.002
type: Parameter

metaid_0000091
unit: 477879
name: sec_inverse
type: SBMLUnitsDef

metaid_0000027
fast: false
reactant: 478421
reactant: 478433
is version of: GO:0043027
reversible: true
type: Reaction
name: cleaved Caspase 9 XIAP binding
is version of: GO:0005515
kinetic law: 478457
product: 478445

metaid_0000013
type: Species
constant: false
has part: P55211
has only substance units: false
initial concentration: 0.0
boundary condition: false
initial amount: NaN
in compartment: metaid_0000086
name: Caspase 9 cleaved-XIAP complex
has part: P98170

metaid_0000030
reversible: false
is version of: GO:0030693
reactant: 478567
type: Reaction
name: Caspase 3 cleavage by cleaved Caspase 9
product: 478603
product: 478591
is: http://identifiers.org/ec-code/3.4.22.62
fast: false
reactant: 478579
kinetic law: 478615

478860
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000040
kinetic law: 478897
reactant: 478885
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 3 cleaved-Xiap degradation
type: Reaction

metaid_0000081
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478001
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

478835
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000050
constant: true
units: metaid_0000089
value: 2.0E-4
type: Parameter

477794
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000012
name: Caspase 3 cleaved - XIAP complex
initial amount: NaN
in compartment: metaid_0000086
has part: P98170
initial concentration: 0.0
boundary condition: false
type: Species
constant: false
has only substance units: false
has part: P42574

metaid_0000026
kinetic law: 478409
product: 478397
reactant: 478385
reactant: 478373
is version of: GO:0005515
fast: false
reversible: true
name: cleaved Caspase 9 Apaf-1 binding
type: Reaction

metaid_0000031
reactant: 478627
type: Reaction
kinetic law: 478675
reversible: false
name: Caspase 3 cleavage by cleaved Caspase 9 - Apaf-1
is version of: GO:0030693
product: 478651
is: http://identifiers.org/ec-code/3.4.22.62
fast: false
product: 478663
reactant: 478639

metaid_0000041
kinetic law: 478921
reactant: 478909
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 9 cleaved-Xiap degradation
type: Reaction

metaid_0000082
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

metaid_0000060
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

metaid_0000061
constant: true
units: metaid_0000089
value: 0.001
type: Parameter

metaid_0000083
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478567
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

477976
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000051
constant: true
units: metaid_0000089
value: 5.0E-5
type: Parameter

478037
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000021
kinetic law: 478145
is version of: GO:0005515
reactant: 478109
reactant: 478121
product: 478133
is version of: GO:0043027
reversible: true
name: Caspase 9-Apaf-1 Xiap binding
fast: false
type: Reaction

478909
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

478217
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

477855
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

477903
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000011
is version of: P42574
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000086
name: Caspase 3 cleaved
type: Species

metaid_0000052
constant: true
units: metaid_0000089
value: 0.0035
type: Parameter

metaid_0000066
constant: true
units: metaid_0000091
value: 0.1
type: Parameter

478531
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

metaid_0000020
name: Caspase 9 Xiap binding
is version of: GO:0043027
product: 478085
reactant: 478073
reactant: 478061
is version of: GO:0005515
fast: false
reversible: true
type: Reaction
kinetic law: 478097

477940
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

478445
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

BIOMD0000000102
reaction: metaid_0000037
parameter: metaid_0000059
parameter: metaid_0000069
reaction: metaid_0000031
curated: true
reaction: metaid_0000041
species: metaid_0000004
is part of: hsa04210
parameter: metaid_0000062
species: metaid_0000005
reaction: metaid_0000034
reaction: metaid_0000044
reaction: metaid_0000027
parameter: metaid_0000071
is version of: GO:0006915
parameter: metaid_0000045
parameter: metaid_0000075
parameter: metaid_0000085
species: metaid_0000012
parameter: metaid_0000070
parameter: metaid_0000072
length unit: length
parameter: metaid_0000078
parameter: metaid_0000055
parameter: metaid_0000065
reaction: metaid_0000038
species: metaid_0000011
parameter: metaid_0000052
parameter: metaid_0000056
species: metaid_0000008
reaction: metaid_0000042
species: metaid_0000009
reaction: metaid_0000017
parameter: metaid_0000080
parameter: metaid_0000049
reaction: metaid_0000021
volume units: metaid_0000004
reaction: metaid_0000024
parameter: metaid_0000046
parameter: metaid_0000063
time units: metaid_0000037
reaction: metaid_0000035
compartment: metaid_0000086
units def: metaid_0000090
parameter: metaid_0000050
species: metaid_0000015
reaction: metaid_0000032
parameter: metaid_0000066
reaction: metaid_0000025
notes: The model reproduces active Caspase-3 time profile corresponding to the total Apaf-1 value of 20 nM as depicted in Fig 2-A . The model was successfully tested on MathSBML.
area units: metaid_0000005
parameter: metaid_0000047
reaction: metaid_0000018
parameter: metaid_0000081
parameter: metaid_0000073
reaction: metaid_0000028
species: metaid_0000010
parameter: metaid_0000079
name: Legewie2006_apoptosis_WT
reaction: metaid_0000022
reaction: metaid_0000039
parameter: metaid_0000076
parameter: metaid_0000053
parameter: metaid_0000057
reaction: metaid_0000043
reaction: metaid_0000036
parameter: metaid_0000058
units def: metaid_0000091
units def: metaid_0000087
reaction: metaid_0000030
is: MODEL8567576821
species: metaid_0000006
reaction: metaid_0000040
species: metaid_0000007
parameter: metaid_0000060
reaction: metaid_0000026
species: metaid_0000016
species: metaid_0000014
is described by: http://identifiers.org/pubmed/16978046
parameter: metaid_0000074

metaid_0000090
unit: 477867
unit: 477855
name: nM
type: SBMLUnitsDef

metaid_0000010
is version of: P42574
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: metaid_0000086
name: Caspase 3
type: Species

478519
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000053
constant: true
units: metaid_0000089
value: 0.002
type: Parameter

478229
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

478603
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

477782
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000067
constant: true
units: metaid_0000089
value: 0.003
type: Parameter

478085
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

477830
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

477867
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

478025
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000023
reactant: 478217
is version of: GO:0005515
kinetic law: 478241
name: cleaved Caspase 3-Xiap binding
product: 478229
reactant: 478205
is version of: GO:0043027
reversible: true
type: Reaction
fast: false

478205
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

478181
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

478810
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000054
constant: true
units: metaid_0000091
value: 0.1
type: Parameter

478121
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

metaid_0000064
constant: true
units: metaid_0000091
value: 0.1
type: Parameter

478933
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

477818
exponent: -1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

478397
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

478543
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000022
kinetic law: 478193
product: 478181
reactant: 478169
reactant: 478157
is version of: GO:0005515
fast: false
reversible: true
name: Caspase 9-Xiap Apaf-1 binding
type: Reaction

477952
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000055
constant: true
units: metaid_0000089
value: 0.001
type: Parameter

477770
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

477891
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

478470
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000065
constant: true
units: metaid_0000089
value: 0.002
type: Parameter

478627
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000077
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478785
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000004
is version of: O14727
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: metaid_0000086
name: APAF-1
type: Species

metaid_0000056
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478336
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

478483
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

478421
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000036
kinetic law: 478798
reactant: 478785
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1-Caspase 9-Xiap degradation
type: Reaction

478385
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

metaid_0000076
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478688
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

metaid_0000005
is version of: P55211
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: metaid_0000086
name: Caspase 9
type: Species

478133
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000057
constant: true
units: metaid_0000089
value: 0.001
type: Parameter

478712
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

478061
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000037
kinetic law: 478823
reactant: 478810
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1-Caspase 9 degradation
type: Reaction

metaid_0000079
constant: true
units: metaid_0000088
value: 0.2
type: Parameter

metaid_0000058
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

metaid_0000068
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478073
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

478288
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000089
unit: 477843
unit: 477830
unit: 477818
name: per_nM_per_sec
type: SBMLUnitsDef

metaid_0000006
constant: false
has part: P55211
in compartment: metaid_0000086
has part: O14727
type: Species
initial amount: NaN
boundary condition: false
name: Caspase 9-XIAP complex
initial concentration: 0.0
has only substance units: false

metaid_0000048
constant: true
units: metaid_0000089
value: 3.5E-4
type: Parameter

478373
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

478495
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

478433
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

477806
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000038
kinetic law: 478848
product: 478835
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 3 turnover
type: Reaction

metaid_0000078
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478349
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000059
constant: true
units: metaid_0000089
value: 0.001
type: Parameter

metaid_0000069
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

metaid_0000007
is version of: P98170
constant: false
boundary condition: false
has only substance units: false
initial concentration: 40.0
initial amount: NaN
in compartment: metaid_0000086
name: XIAP
type: Species

metaid_0000088
unit: 477806
unit: 477794
unit: 477782
name: nM_per_sec
type: SBMLUnitsDef

metaid_0000049
constant: true
units: metaid_0000089
value: 2.0E-4
type: Parameter

477843
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000039
kinetic law: 478873
reactant: 478860
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 3 cleaved degradation
type: Reaction

metaid_0000087
unit: 477770
name: nanomole
type: SBMLUnitsDef

metaid_0000008
has part: P98170
initial concentration: 0.0
name: APAF-1-Caspase 9-XIAP complex
constant: false
has part: P55211
initial amount: NaN
boundary condition: false
has part: O14727
type: Species
in compartment: metaid_0000086
has only substance units: false

metaid_0000073
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478579
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

478276
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000018
fast: false
is: http://identifiers.org/ec-code/3.4.22.62
product: 477964
reactant: 477952
product: 477976
type: Reaction
kinetic law: 477989
is version of: GO:0030693
reversible: false
reactant: 477940
name: Caspase 3 cleavage by Caspase 9
is version of: GO:0006919

478885
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000046
constant: true
units: metaid_0000091
value: 0.1
type: Parameter

metaid_0000070
constant: true
units: metaid_0000088
value: 0.02
type: Parameter

478663
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000028
reversible: true
reactant: 478483
is version of: GO:0043027
reactant: 478470
is version of: GO:0005515
fast: false
type: Reaction
product: 478495
name: cleaved Caspase 9-Apaf-1 XIAP binding
kinetic law: 478507

478312
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000032
kinetic law: 478700
product: 478688
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1 turnover
type: Reaction

metaid_0000086
is: GO:0005829
constant: true
size: 1.0
spatial dimensions: 3.0
name: Cytosol
type: Compartment

metaid_0000009
has only substance units: false
initial concentration: 0.0
name: APAF-1-Caspase 9 complex
has part: P55211
boundary condition: false
constant: false
initial amount: NaN
type: Species
has part: O14727
in compartment: metaid_0000086

metaid_0000072
constant: true
units: metaid_0000088
value: 0.02
type: Parameter

metaid_0000019
product: 478025
reversible: false
kinetic law: 478049
type: Reaction
reactant: 478001
fast: false
name: Caspase 3 cleavage by Caspase 9-Apaf-1
product: 478037
reactant: 478013
is version of: GO:0006919

metaid_0000071
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478157
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

478591
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

478760
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

478736
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

metaid_0000047
constant: true
units: metaid_0000089
value: 5.0E-6
type: Parameter

metaid_0000033
kinetic law: 478724
product: 478712
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 9 turnover
type: Reaction

metaid_0000029
kinetic law: 478555
product: 478543
reactant: 478531
reactant: 478519
is version of: GO:0005515
fast: false
reversible: true
name: cleaved Caspase 9-Xiap Apaf-1 binding
type: Reaction

478639
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000085
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

metaid_0000075
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

478109
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000016
type: Species
name: Apaf-1-Caspase 9 cleaved -XIAP complex
initial amount: NaN
constant: false
has only substance units: false
has part: P98170
in compartment: metaid_0000086
initial concentration: 0.0
boundary condition: false
has part: O14727
has part: P55211

metaid_0000044
kinetic law: 478994
reactant: 478982
is version of: GO:0044257
fast: false
reversible: false
name: Apaf-1 Caspase 9 cleaved-Xiap degradation
type: Reaction

478324
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000034
kinetic law: 478748
product: 478736
is version of: GO:0044257
fast: false
reversible: false
name: Xiap turnover
type: Reaction

metaid_0000084
constant: true
units: metaid_0000091
value: 0.001
type: Parameter

metaid_0000074
constant: true
units: metaid_0000088
value: 0.04
type: Parameter

metaid_0000017
kinetic law: 477928
product: 477916
reactant: 477903
reactant: 477891
is version of: GO:0005515
fast: false
reversible: true
name: Caspase 9 / Apaf-1 binding
type: Reaction

metaid_0000045
constant: true
units: metaid_0000089
value: 0.002
type: Parameter

metaid_0000035
kinetic law: 478773
reactant: 478760
is version of: GO:0044257
fast: false
reversible: false
name: Caspase 9-Xiap degradation
type: Reaction

478253
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

478982
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

478169
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

given: Nils
family: Bluethgen

orgname: Humboldt University Berlin

orgname: Humboldt University Berlin

W3 CDTF: Sat Apr 21 00:21:36 BST 2012

W3 CDTF: Thu Apr 20 11:59:50 BST 2006

given: Stefan
family: Legewie

given: Harish
family: Dharuri

ORG:
  orgname: California Institute of Technology

ORG:
  orgname: Humboldt Universtity Berlin
n:
  given: Hanspeter
  family: Herzel