BIOMD0000000106
type: SBMLModel
parameter: metaid_0000032
parameter: metaid_0000027
parameter: metaid_0000012
reaction: metaid_0000111
species: metaid_0000070
parameter: metaid_0000054
parameter: metaid_0000056
reaction: metaid_0000109
species: metaid_0000072
parameter: metaid_0000035
species: metaid_0000071
parameter: metaid_0000015
reaction: metaid_0000092
species: metaid_0000082
reaction: metaid_0000095
units def: metaid_0000112
parameter: metaid_0000004
parameter: metaid_0000028
is version of: GO:0019369
parameter: metaid_0000007
name: Yang2007_ArachidonicAcid
species: metaid_0000069
species: metaid_0000068
length unit: length
notes: This model is according to the paper Dynamic Simulation on the Arachidonic Acid Metabolic Network . Figure 2A has been reproduced by SBML ode solver on line. In the original model, all the reactions are presented as ODE directly. So curator rewrite each reaction according to the semantics of the paper. In this paper, the authors used quict complex kinetics law to describe the catalysis in the network, curators did not necessarily know all the complete meanings of the paper. 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_0000020
species: metaid_0000065
parameter: metaid_0000038
parameter: metaid_0000016
reaction: metaid_0000117
parameter: metaid_0000023
species: metaid_0000077
parameter: metaid_0000050
parameter: metaid_0000019
reaction: metaid_0000105
time units: metaid_0000114
parameter: metaid_0000011
reaction: metaid_0000110
is described by: http://identifiers.org/pubmed/17381237
reaction: metaid_0000108
reaction: metaid_0000086
species: metaid_0000060
parameter: metaid_0000041
species: metaid_0000078
reaction: metaid_0000089
parameter: metaid_0000046
parameter: metaid_0000031
parameter: metaid_0000026
parameter: metaid_0000053
species: metaid_0000061
parameter: metaid_0000049
parameter: metaid_0000034
parameter: metaid_0000014
reaction: metaid_0000113
reaction: metaid_0000091
species: metaid_0000074
parameter: metaid_0000037
species: metaid_0000073
reaction: metaid_0000121
reaction: metaid_0000116
reaction: metaid_0000094
reaction: metaid_0000097
reaction: metaid_0000104
parameter: metaid_0000006
is: MODEL8610058649
substance units: metaid_0000112
parameter: metaid_0000009
parameter: metaid_0000040
parameter: metaid_0000022
species: metaid_0000067
species: metaid_0000066
parameter: metaid_0000018
reaction: metaid_0000119
species: metaid_0000063
parameter: metaid_0000043
parameter: metaid_0000045
parameter: metaid_0000025
parameter: metaid_0000010
species: metaid_0000079

metaid_0000032
type: Parameter
constant: true
value: 0.3

metaid_0000027
type: Parameter
constant: true
value: 0.001

metaid_0000012
type: Parameter
constant: true
value: 3000.0
name: Kcat(PGES)

metaid_0000111
type: Reaction
kinetic law: 080158
reactant: 080146
is version of: GO:0044248
fast: false
reversible: false
name: 15-HETE decay

080146
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000077

metaid_0000077
type: Species
in compartment: metaid_0000058
has only substance units: false
constant: false
initial concentration: 0.001
is: C04742
is: CHEBI:15558
name: 15-HETE
initial amount: NaN
boundary condition: false

metaid_0000058
type: Compartment
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

metaid_0000070
type: Species
boundary condition: false
initial concentration: 0.001
is: C05966
has only substance units: false
in compartment: metaid_0000058
constant: false
name: 15-HPETE
is: CHEBI:15628
initial amount: NaN

metaid_0000054
type: Parameter
constant: true
value: 2.3E-5

metaid_0000056
type: Parameter
constant: true
value: 500.0

metaid_0000109
type: Reaction
kinetic law: 080110
reactant: 080098
is version of: GO:0044248
fast: false
reversible: false
name: LTB4 decay

080098
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000063

metaid_0000063
type: Species
is: CHEBI:15647
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000058
name: LTB4

metaid_0000072
type: Species
is: P09917
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0
initial amount: NaN
in compartment: metaid_0000058
name: 5-LOX

metaid_0000035
type: Parameter
constant: true
value: 0.6

metaid_0000071
type: Species
is: P24557
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.5
initial amount: NaN
in compartment: metaid_0000058
name: TXAS

metaid_0000015
type: Parameter
constant: true
value: 4.0
name: Km(TXAS)

metaid_0000092
type: Reaction
kinetic law: 079459
modifier: 079447
product: 079435
fast: false
reversible: false
name: TXB2 production

metaid_0000082
type: Species
name: TXA2
initial concentration: 0.001
initial amount: NaN
constant: false
in compartment: metaid_0000058
has only substance units: false
is: CHEBI:15627
boundary condition: false
is: C02198

079435
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000083

metaid_0000083
type: Species
constant: false
has only substance units: false
in compartment: metaid_0000058
is: C05963
is: CHEBI:28728
initial amount: NaN
initial concentration: 0.001
boundary condition: false
name: TXB2

metaid_0000095
type: Reaction
modifier: 079664
modifier: 079688
is version of: http://identifiers.org/ec-code/1.13.11.34
name: LTA4 production
modifier: 079640
kinetic law: 079700
product: 079628
reversible: true
modifier: 079676
modifier: 079652
is version of: GO:0004051
reactant: 079616
fast: false

metaid_0000081
type: Species
is: CHEBI:15551
initial concentration: 0.001
initial amount: NaN
constant: false
boundary condition: false
in compartment: metaid_0000058
has only substance units: false
name: PGE2
is: C00584

metaid_0000061
type: Species
in compartment: metaid_0000058
is: CHEBI:28209
initial concentration: 0.001
is: C04805
boundary condition: false
name: 5-HETE
has only substance units: false
constant: false
initial amount: NaN

079628
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

metaid_0000062
type: Species
is: CHEBI:15651
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000058
name: LTA4

metaid_0000079
type: Species
boundary condition: false
in compartment: metaid_0000058
is: CHEBI:34146
has only substance units: false
initial concentration: 0.001
name: 12-HETE
is: C14777
initial amount: NaN
constant: false

079616
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000060

metaid_0000060
type: Species
name: 5-HPETE
is: C05356
boundary condition: false
in compartment: metaid_0000058
constant: false
initial concentration: 0.001
has only substance units: false
initial amount: NaN
is: CHEBI:15632

metaid_0000112
type: SBMLUnitsDef
unit: 078941
name: micromole

078941
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

metaid_0000004
type: Parameter
notes: upper case K
constant: true
value: 3600.0
name: Kcat(PLA2)

metaid_0000028
type: Parameter
constant: true
value: 0.001

metaid_0000007
type: Parameter
constant: true
value: 70.0
name: Km(15-LOX)

metaid_0000069
type: Species
is: Q9H7Z7
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.5
initial amount: NaN
in compartment: metaid_0000058
name: PGES

metaid_0000068
type: Species
is version of: P35354
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.2
initial amount: NaN
in compartment: metaid_0000058
name: COX-2

metaid_0000020
type: Parameter
constant: true
value: 150.0
name: Kcat(CYP4F3)

metaid_0000065
type: Species
is: P04054
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.5
initial amount: NaN
in compartment: metaid_0000058
name: PLA2

metaid_0000038
type: Parameter
constant: true
value: 30.0

metaid_0000016
type: Parameter
constant: true
value: 5000.0
name: Kcat(5-LOX)

metaid_0000117
type: Reaction
kinetic law: 080266
modifier: 080254
reactant: 080242
is version of: GO:0043086
fast: false
reversible: false
name: 5-LOX inhibition by x12

080242
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000072

metaid_0000023
type: Parameter
constant: true
value: 70.0
name: Km(PHGPx)

metaid_0000050
type: Parameter
constant: true
value: 200.0

metaid_0000019
type: Parameter
constant: true
value: 20.0
name: Km(LTA4H)

metaid_0000105
type: Reaction
kinetic law: 080002
modifier: 079990
reactant: 079978
is version of: GO:0043086
fast: false
reversible: false
name: LTA4H inhibition

079978
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000073

metaid_0000073
type: Species
is: P09960
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.76
initial amount: NaN
in compartment: metaid_0000058
name: LTA4H

metaid_0000114
type: SBMLUnitsDef
unit: 078953
name: minute

078953
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid_0000011
type: Parameter
constant: true
value: 50.0
name: Km(COX-2)

metaid_0000110
type: Reaction
kinetic law: 080134
reactant: 080122
is version of: GO:0044248
fast: false
reversible: false
name: LTA4 decay

080122
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

metaid_0000108
type: Reaction
kinetic law: 080086
reactant: 080074
is version of: GO:0044248
fast: false
reversible: false
name: TAX2 decay

080074
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000082

metaid_0000086
type: Reaction
reactant: 079098
is version of: GO:0047066
name: 15-HETE production
fast: false
reversible: true
modifier: 079122
kinetic law: 079134
is version of: http://identifiers.org/ec-code/1.11.1.12
product: 079110

079098
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000070

metaid_0000075
type: Species
is: P36969
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.8
initial amount: NaN
in compartment: metaid_0000058
name: PHGPx

079110
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000077

metaid_0000041
type: Parameter
constant: true
value: 0.01

metaid_0000078
type: Species
initial amount: NaN
is: C05965
constant: false
in compartment: metaid_0000058
name: 12-HPETE
is: CHEBI:15626
has only substance units: false
initial concentration: 0.001
boundary condition: false

metaid_0000089
type: Reaction
modifier: 079279
fast: false
product: 079267
is version of: http://identifiers.org/ec-code/1.14.99.1
kinetic law: 079303
modifier: 079291
reversible: true
reactant: 079255
is version of: GO:0004666
name: PGH2 production

079267
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000080

metaid_0000080
type: Species
has only substance units: false
initial amount: NaN
is: CHEBI:15554
in compartment: metaid_0000058
constant: false
is: C00427
boundary condition: false
name: PGH2
initial concentration: 0.001

079255
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000059
type: Species
boundary condition: false
initial amount: NaN
is: C00219
constant: false
is: CHEBI:15843
has only substance units: false
name: AA
in compartment: metaid_0000058
initial concentration: 0.001

metaid_0000046
type: Parameter
constant: true
value: 10.0

metaid_0000031
type: Parameter
constant: true
value: 0.01

metaid_0000026
type: Parameter
constant: true
value: 0.1

metaid_0000053
type: Parameter
constant: true
value: 0.053

metaid_0000049
type: Parameter
constant: true
value: 500.0

metaid_0000034
type: Parameter
constant: true
value: 30.0

metaid_0000014
type: Parameter
constant: true
value: 1599.0
name: Kcat(TXAS)

metaid_0000113
type: Reaction
kinetic law: 080182
reactant: 080170
is version of: GO:0044248
fast: false
reversible: false
name: 15-HPETE decay

080170
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000070

metaid_0000091
type: Reaction
fast: false
is version of: GO:0004796
kinetic law: 079423
reversible: true
reactant: 079387
product: 079399
is version of: http://identifiers.org/ec-code/5.3.99.5
name: TXA2 production
modifier: 079411

079387
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000080

079399
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000082

metaid_0000074
type: Species
is: Q08477
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.07
initial amount: NaN
in compartment: metaid_0000058
name: CYP4F3

metaid_0000037
type: Parameter
constant: true
value: 0.01

metaid_0000121
type: Reaction
kinetic law: 080364
reactant: 080352
is version of: GO:0044248
fast: false
reversible: false
name: AA decay

080352
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000116
type: Reaction
kinetic law: 080230
reactant: 080218
is version of: GO:0044248
fast: false
reversible: false
name: 5-HETE decay

080218
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000061

metaid_0000094
type: Reaction
fast: false
kinetic law: 079604
is version of: GO:0047066
reversible: true
name: 5-HETE production
modifier: 079592
is version of: http://identifiers.org/ec-code/1.11.1.12
product: 079580
reactant: 079568

079580
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000061

079568
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000060

metaid_0000097
type: Reaction
kinetic law: 079821
is version of: http://identifiers.org/ec-code/1.14.13.30
product: 079772
modifier: 079809
modifier: 079784
reversible: true
reactant: 079760
modifier: 079796
is version of: GO:0050051
fast: false
name: 20-OH-LTB4 production

079772
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000064

metaid_0000064
type: Species
is: CHEBI:15646
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000058
name: w-LTB4

079760
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000063

metaid_0000104
type: Reaction
kinetic law: 079966
modifier: 079954
product: 079942
is version of: GO:0043085
fast: false
reversible: false
name: 5-LOX upregulation

079942
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000072

metaid_0000006
type: Parameter
constant: true
value: 1000.0
name: Kcat(15-LOX)

metaid_0000009
type: Parameter
constant: true
value: 50.0
name: Km(12-LOX)

metaid_0000040
type: Parameter
constant: true
value: 0.175

metaid_0000022
type: Parameter
constant: true
value: 500.0
name: Kcat(PHGPx)

metaid_0000067
type: Species
is: P18054
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.5
initial amount: NaN
in compartment: metaid_0000058
name: 12-LOX

metaid_0000066
type: Species
is: P16050
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.5
initial amount: NaN
in compartment: metaid_0000058
name: 15-LOX

metaid_0000018
type: Parameter
constant: true
value: 125.0
name: Kcat(LTA4H)

metaid_0000119
type: Reaction
kinetic law: 080340
modifier: 080328
reactant: 080315
is version of: GO:0043086
fast: false
reversible: false
name: 5-LOX inhibition by x2

080315
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000072

metaid_0000043
type: Parameter
constant: true
value: 6.3

metaid_0000045
type: Parameter
constant: true
value: 0.86

metaid_0000025
type: Parameter
constant: true
value: 0.01

metaid_0000010
type: Parameter
constant: true
value: 1000.0
name: Kcat(COX-2)

metaid_0000052
type: Parameter
constant: true
value: 500.0

metaid_0000107
type: Reaction
kinetic law: 080062
modifier: 080050
reactant: 080038
is version of: GO:0043086
fast: false
reversible: false
name: TXAS inhibition by PGH2

080038
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000071

metaid_0000085
type: Reaction
reactant: 079049
fast: false
is version of: GO:0050473
kinetic law: 079086
modifier: 079073
name: 15-HPETE production
is version of: http://identifiers.org/ec-code/1.13.11.33
product: 079061
reversible: true

079049
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

079061
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000070

metaid_0000033
type: Parameter
constant: true
value: 30.0

metaid_0000013
type: Parameter
constant: true
value: 160.0
name: Km(PGES)

metaid_0000090
type: Reaction
name: PGE2 production
modifier: 079339
modifier: 079363
is version of: http://identifiers.org/ec-code/5.3.99.3
product: 079327
reversible: true
reactant: 079315
is version of: GO:0050220
kinetic law: 079375
fast: false
modifier: 079351

079327
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000081

079315
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000080

metaid_0000055
type: Parameter
constant: true
value: 0.15

metaid_0000088
type: Reaction
reactant: 079207
modifier: 079231
name: 12-HETE production
kinetic law: 079243
is version of: http://identifiers.org/ec-code/1.11.1.12
reversible: true
fast: false
is version of: GO:0047066
product: 079219

079207
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000078

079219
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000079

W3 CDTF: Thu Jul 05 15:48:14 BST 2012

metaid_0000100
type: Reaction
kinetic law: 079894
modifier: 079882
reactant: 079870
is version of: GO:0043086
fast: false
reversible: false
name: 12-LOX inhibition

079870
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000067

metaid_0000096
type: Reaction
reactant: 079712
kinetic law: 079748
modifier: 079736
product: 079724
fast: false
is version of: http://identifiers.org/ec-code/3.3.2.6
is version of: GO:0004463
name: LTB4 production
reversible: true

079712
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

079724
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000063

metaid_0000048
type: Parameter
constant: true
value: 10.0

metaid_0000005
type: Parameter
notes: lower case k
constant: true
value: 2600.0
name: Km(PLA2)

metaid_0000099
type: Reaction
kinetic law: 079858
modifier: 079845
product: 079833
is version of: GO:0045893
fast: false
reversible: false
name: 15-LOX upregulation

079833
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000066

metaid_0000029
type: Parameter
constant: true
value: 0.07

metaid_0000036
type: Parameter
constant: true
value: 0.1

metaid_0000115
type: Reaction
kinetic law: 080206
reactant: 080194
is version of: GO:0030163
fast: false
reversible: false
name: 15-LOX decay

080194
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000066

metaid_0000093
type: Reaction
is version of: GO:0004051
reactant: 079471
is version of: http://identifiers.org/ec-code/1.13.11.34
reversible: true
modifier: 079544
kinetic law: 079556
modifier: 079532
modifier: 079520
modifier: 079508
product: 079483
name: 5-HPETE production
modifier: 079495
fast: false

079471
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

079483
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000060

metaid_0000021
type: Parameter
constant: true
value: 3.9
name: Km(CYP4F3)

metaid_0000039
type: Parameter
constant: true
value: 4.0

metaid_0000017
type: Parameter
constant: true
value: 5.0
name: Km(5-LOX)

metaid_0000118
type: Reaction
kinetic law: 080302
modifier: 080290
reactant: 080278
is version of: GO:0043086
fast: false
reversible: false
name: 5-LOX inhibition by x10

080278
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000072

metaid_0000103
type: Reaction
kinetic law: 079930
modifier: 079918
reactant: 079906
is version of: GO:0043086
fast: false
reversible: false
name: TXAS inhibition

079906
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000071

metaid_0000106
type: Reaction
kinetic law: 080026
reactant: 080014
is version of: GO:0044248
fast: false
reversible: false
name: TXB2 decay

080014
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000083

metaid_0000084
type: Reaction
reversible: false
product: 078965
kinetic law: 079037
modifier: 079025
is version of: http://identifiers.org/ec-code/3.1.1.4
modifier: 078989
name: AA production
modifier: 079001
fast: false
modifier: 078977
is version of: GO:0004623
modifier: 079013

078965
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000008
type: Parameter
constant: true
value: 1000.0
name: Kcat(12-LOX)

metaid_0000076
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000058
name: exo-AA

metaid_0000087
type: Reaction
is version of: GO:0004052
fast: false
product: 079159
name: 12-HPETE production
modifier: 079183
modifier: 079171
is version of: http://identifiers.org/ec-code/1.13.11.31
reactant: 079146
kinetic law: 079195
reversible: true

079159
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000078

079146
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000042
type: Parameter
constant: true
value: 15.0

metaid_0000044
type: Parameter
constant: true
value: 0.2

metaid_0000024
type: Parameter
constant: true
value: 0.05

metaid_0000003
type: Parameter
constant: true
value: 12.0
name: lin

metaid_0000051
type: Parameter
constant: true
value: 500.0

metaid_0000047
type: Parameter
constant: true
value: 10.0

metaid_0000030
type: Parameter
constant: true
value: 0.01

ORG:
  orgname: Beijing National Laboratory for Molecular Sciences
n:
  given: Kun
  family: Yang

W3 CDTF: Fri Jan 12 15:06:16 GMT 2007

ORG:
  orgname: BNMC
n:
  given: Enuo
  family: He