BIOMD0000000336
type: SBMLModel
reaction: 27
parameter: 46
notes: This model is from the article: A model for the tissue factor pathway to thrombin. II. A mathematical simulation. Jones KC, Mann KG. J Biol Chem. 1994 Sep 16;269(37):23367-73. 8083242 , Abstract: A mathematical simulation of the tissue factor pathway to the generation of thrombin has been developed using a combination of empirical, estimated, and deduced rate constants for reactions involving the activation of factor IX, X, V, and VIII, in the formation of thrombin, as well as rate constants for the assembly of the coagulation enzyme complexes which involve factor VIIIa-factor IXa (intrinsic tenase) and factor Va-Xa (prothrombinase) assembled on phospholipid membrane. Differential equations describing the fate of each species in the reaction were developed and solved using an interactive procedure based upon the Runge-Kutta technique. In addition to the theoretical considerations involving the reactions of the tissue factor pathway, a physical constraint associated with the stability of the factor VIIIa-factor IXa complex has been incorporated into the model based upon the empirical observations associated with the stability of this complex. The model system provides a realistic accounting of the fates of each of the proteins in the coagulation reaction through a range of initiator (factor VIIa-tissue factor) concentrations ranging from 5 pM to 5 nM. The model is responsive to alterations in the concentrations of factor VIII, factor V, and their respective activated species, factor VIIIa and factor Va, and overall provides a reasonable approximation of empirical data. The computer model permits the assessment of the reaction over a broad range of conditions and provides a useful tool for the development and management of reaction studies. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. For more information see the terms of use . To cite Bi…
parameter: 51
is described by: http://identifiers.org/pubmed/8083242
parameter: 49
species: 3
species: 9
reaction: 30
reaction: 33
species: 14
parameter: 54
reaction: 21
parameter: 57
parameter: 42
function def: 62
rule: 64
is version of: GO:0007596
species: 5
parameter: 45
rule: 63
reaction: 38
reaction: 36
time units: 858180
reaction: 24
reaction: 26
reaction: 29
species: 15
parameter: 50
parameter: 48
compartment: 61
parameter: 53
curated: true
occurs in: http://identifiers.org/taxonomy/2759
parameter: 41
reaction: 32
length unit: length
creator:
  ORG:
    orgname: EBI
  n:
    given: Michael
    family: Schubert
substance units: metaid_0000254
reaction: 35
reaction: 20
species: 11
species: 10
created:
  W3 CDTF: Mon Jun 06 18:21:19 BST 2011
parameter: 56
parameter: 39
reaction: 23
species: 6
parameter: 59
parameter: 44
is: MODEL1106060000
parameter: 47
species: 1
volume units: 858228
reaction: 28
reaction: 31
species: 2
species: 17
species: 16
parameter: 52
species: 8
parameter: 60
parameter: 55
parameter: 40
parameter: 43
reaction: 34
species: 7
name: Jones1994_BloodCoagulation
area units: area
reaction: 37
reaction: 22
species: 13
reaction: 19
species: 12
species: 4
parameter: 58
name: function_4_VIIIa_IXa_degradation_2
species: 18
reaction: 25

27
type: Reaction
kinetic law: 040999
product: 040987
product: 040975
reactant: 040963
reactant: 040951
fast: false
reversible: false
name: R6

040987
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 13

13
type: Species
is version of: P00451
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 61
name: VIIIa

61
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment_1

040975
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 7

7
type: Species
is version of: P00742
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 61
name: Xa

040963
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 7

040951
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 12

12
type: Species
is: P00451
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.0E-10
initial amount: NaN
in compartment: 61
name: VIII

46
type: Parameter
constant: true
value: 4.0E8
name: k8

51
type: Parameter
is: SBO:0000035
constant: true
value: 8.2
name: k13

49
type: Parameter
is: SBO:0000035
constant: true
value: 0.3
name: k11

3
type: Species
has part: P13726
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0E-9
initial amount: NaN
in compartment: 61
name: TF_VIIa

9
type: Species
name: X_VIIIa_IXa
initial amount: NaN
constant: false
has only substance units: false
initial concentration: 0.0
has part: P00740
has part: P00742
has part: P00451
boundary condition: false
in compartment: 61

30
type: Reaction
kinetic law: 041168
product: 041156
reactant: 041144
reactant: 041132
fast: false
reversible: true
name: R9

041156
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 16

16
type: Species
initial concentration: 0.0
in compartment: 61
has part: P00734
name: II_Va_Xa
has part: P12259
constant: false
boundary condition: false
has only substance units: false
initial amount: NaN
has part: P00742

041144
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 17

17
type: Species
has only substance units: false
has part: P12259
in compartment: 61
name: Va_Xa
boundary condition: false
has part: P00742
constant: false
initial concentration: 0.0
initial amount: NaN

041132
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 15

15
type: Species
is: P00734
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.4E-6
initial amount: NaN
in compartment: 61
name: II

33
type: Reaction
kinetic law: 041324
product: 041312
reactant: 041300
reactant: 041288
fast: false
reversible: true
name: R11

041312
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 8

8
type: Species
has part: P00451
initial concentration: 0.0
in compartment: 61
initial amount: NaN
has part: P00740
constant: false
has only substance units: false
boundary condition: false
name: VIIIa_IXa

041300
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 4

4
type: Species
is version of: P00740
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 61
name: IXa

041288
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 13

14
type: Species
is version of: P00734
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 61
name: IIa

54
type: Parameter
is: SBO:0000038
constant: true
value: 24.0
name: k16

21
type: Reaction
kinetic law: 040671
product: 040659
reactant: 040647
reactant: 040634
fast: false
reversible: true
name: R2

040659
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 6

6
type: Species
in compartment: 61
has part: P13726
boundary condition: false
has only substance units: false
has part: P00742
initial amount: NaN
constant: false
initial concentration: 0.0
name: X_TF_VIIa

040647
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 3

040634
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 5

5
type: Species
is: P00742
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.7E-7
initial amount: NaN
in compartment: 61
name: X

57
type: Parameter
is: SBO:0000038
constant: true
value: 70.0
name: k19

42
type: Parameter
is: SBO:0000036
constant: true
value: 2.0E7
name: k4

45
type: Parameter
is: SBO:0000036
constant: true
value: 1.0E7
name: k7

38
type: Reaction
kinetic law: 041590
modifier: 041578
reactant: 041565
fast: false
reversible: false
name: VIIIa_IXa_degradation

041565
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 8

36
type: Reaction
kinetic law: 041493
product: 041481
product: 041469
reactant: 041457
reactant: 041445
fast: false
reversible: false
name: R8_atn

041481
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 13

041469
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 18

18
type: Species
is version of: P00734
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 61
name: mIIa

041457
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 18

041445
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 12

24
type: Reaction
kinetic law: 040817
product: 040805
product: 040793
reactant: 040781
fast: false
reversible: false
name: R3b

040805
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 7

040793
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 8

040781
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 9

26
type: Reaction
kinetic law: 040939
product: 040927
product: 040914
reactant: 040902
reactant: 040890
fast: false
reversible: false
name: R5

040927
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 11

11
type: Species
is version of: P12259
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 61
name: Va

040914
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 7

040902
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 7

040890
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 10

10
type: Species
is: P12259
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.0E-8
initial amount: NaN
in compartment: 61
name: V

29
type: Reaction
kinetic law: 041119
product: 041107
product: 041095
reactant: 041083
reactant: 041071
fast: false
reversible: false
name: R8

041107
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 13

041095
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 14

041083
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 14

041071
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 12

50
type: Parameter
is: SBO:0000035
constant: true
value: 1.15
name: k12

48
type: Parameter
is: SBO:0000038
constant: true
value: 0.4
name: k10

53
type: Parameter
is: SBO:0000036
constant: true
value: 100000.0
name: k15

41
type: Parameter
is: SBO:0000036
constant: true
value: 1.0E7
name: k3

32
type: Reaction
kinetic law: 041276
product: 041264
product: 041252
reactant: 041240
reactant: 041228
fast: false
reversible: false
name: R10

041264
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 14

041252
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 17

041240
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 17

041228
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 18

35
type: Reaction
kinetic law: 041433
product: 041420
product: 041408
reactant: 041396
reactant: 041384
fast: false
reversible: false
name: R7_atn

041420
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 11

041408
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 18

041396
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 18

041384
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 10

20
type: Reaction
kinetic law: 040622
product: 040610
product: 040598
reactant: 040586
fast: false
reversible: false
name: R1b

040610
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 4

040598
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 3

040586
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 2

2
type: Species
constant: false
initial concentration: 0.0
boundary condition: false
has part: P13726
initial amount: NaN
has only substance units: false
in compartment: 61
has part: P00740
name: IX_TF_VIIa

56
type: Parameter
is: SBO:0000038
constant: true
value: 0.001
name: k18

39
type: Parameter
is: SBO:0000036
constant: true
value: 2.0E7
name: k1

23
type: Reaction
kinetic law: 040769
product: 040757
reactant: 040745
reactant: 040733
fast: false
reversible: true
name: R3

040757
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 9

040745
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 8

040733
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 5

59
type: Parameter
constant: false
value: 0.0
name: I

44
type: Parameter
is: SBO:0000036
constant: true
value: 1.0E8
name: k6

47
type: Parameter
is: SBO:0000038
constant: true
value: 0.005
name: k9

1
type: Species
is: P00740
constant: false
boundary condition: false
has only substance units: false
initial concentration: 9.0E-8
initial amount: NaN
in compartment: 61
name: IX

28
type: Reaction
kinetic law: 041059
product: 041047
product: 041035
reactant: 041023
reactant: 041011
fast: false
reversible: false
name: R7

041047
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 11

041035
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 14

041023
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 14

041011
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 10

31
type: Reaction
kinetic law: 041216
product: 041204
product: 041192
reactant: 041180
fast: false
reversible: false
name: R9b

041204
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 18

041192
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 17

041180
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 16

52
type: Parameter
is: SBO:0000035
constant: true
value: 32.0
name: k14

60
type: Parameter
constant: false
value: 0.0
name: IIa+1.2mIIa

55
type: Parameter
is: SBO:0000038
constant: true
value: 44.0
name: k17

40
type: Parameter
is: SBO:0000036
constant: true
value: 2.0E7
name: k2

43
type: Parameter
is: SBO:0000036
constant: true
value: 1.0E7
name: k5

34
type: Reaction
kinetic law: 041372
product: 041360
reactant: 041348
reactant: 041336
fast: false
reversible: true
name: R12

041360
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 17

041348
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 7

041336
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 11

37
type: Reaction
kinetic law: 041553
product: 041541
product: 041529
reactant: 041517
reactant: 041505
fast: false
reversible: false
name: R4_atn

041541
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 4

041529
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 17

041517
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 17

041505
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 1

22
type: Reaction
kinetic law: 040721
product: 040709
product: 040697
reactant: 040684
fast: false
reversible: false
name: R2b

040709
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 7

040697
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 3

040684
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 6

19
type: Reaction
kinetic law: 040574
product: 040562
reactant: 040550
reactant: 040538
fast: false
reversible: true
name: R1

040562
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 2

040550
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 3

040538
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 1

58
type: Parameter
constant: true
value: 0.02
name: k20

25
type: Reaction
kinetic law: 040878
product: 040865
product: 040853
reactant: 040841
reactant: 040829
fast: false
reversible: false
name: R4

040865
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: 4

040853
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 7

040841
type: SpeciesReference
is: SBO:0000461
stoichiometry: 1.0
species: 7

040829
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: 1

W3 CDTF: Fri Apr 20 22:53:01 BST 2012