BIOMD0000000102
type: SBMLModel
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

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

478810
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000009
type: Species
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
has part: O14727
in compartment: metaid_0000086

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

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

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

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

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

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

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

metaid_0000091
type: SBMLUnitsDef
unit: 477879
name: sec_inverse

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

metaid_0000031
type: Reaction
reactant: 478627
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

478627
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000010
type: Species
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

478651
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000011
type: Species
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

478663
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

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

478639
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

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

478909
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

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_0000004
type: Species
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

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

metaid_0000005
type: Species
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

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

478736
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

metaid_0000007
type: Species
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

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

478982
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

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_0000027
type: Reaction
fast: false
reactant: 478421
reactant: 478433
is version of: GO:0043027
reversible: true
name: cleaved Caspase 9 XIAP binding
is version of: GO:0005515
kinetic law: 478457
product: 478445

478421
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000014
type: Species
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

478433
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

478445
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

478835
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

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

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

metaid_0000008
type: Species
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
in compartment: metaid_0000086
has only substance units: false

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

478933
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

477916
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

477903
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

477891
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

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

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

metaid_0000021
type: Reaction
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

478109
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

478121
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

478133
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

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

478265
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

478288
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

478253
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

478276
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

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

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

478760
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

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

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

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

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

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

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

478688
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

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

metaid_0000025
type: Reaction
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
kinetic law: 478361

478349
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

478336
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

478324
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

478312
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

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

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

477964
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

477952
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

477976
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

477940
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

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

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

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

478483
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

478470
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

478495
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

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

metaid_0000022
type: Reaction
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

478181
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

478169
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

478157
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

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

478860
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

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

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

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

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

478958
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

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

478785
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

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

metaid_0000087
type: SBMLUnitsDef
unit: 477770
name: nanomole

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

metaid_0000030
type: Reaction
reversible: false
is version of: GO:0030693
reactant: 478567
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

478567
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

478603
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

478591
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

478579
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

478885
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

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

metaid_0000026
type: Reaction
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

478397
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

478385
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

478373
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

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

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

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

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

478712
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

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

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

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

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

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

478025
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

478001
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

478037
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

478013
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

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

metaid_0000029
type: Reaction
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

478543
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

478531
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

478519
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

metaid_0000023
type: Reaction
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
fast: false

478217
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

478229
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

478205
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

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

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

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

metaid_0000020
type: Reaction
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
kinetic law: 478097

478085
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

478073
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

478061
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

ORG:
  orgname: Humboldt University Berlin
n:
  given: Nils
  family: Bluethgen

ORG:
  orgname: Humboldt University Berlin
n:
  given: Stefan
  family: Legewie

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

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

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

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