BioModels Database logo

BioModels Database

spacer

BIOMD0000000106 - Yang2007_ArachidonicAcid

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 17381237
Yang K, Ma W, Liang H, Ouyang Q, Tang C, Lai L.
Dynamic simulations on the arachidonic acid metabolic network.
PLoS Comput. Biol. 2007 Mar; 3(3): e55
Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.  [more]
Model
Original Model: BIOMD0000000106.xml.origin
Submitter: Kun Yang
Submission ID: MODEL8610058649
Submission Date: 09 Apr 2007 19:28:33 UTC
Last Modification Date: 05 Jul 2012 14:48:14 UTC
Creation Date: 12 Jan 2007 15:06:16 UTC
Encoders:  Enuo He
   Kun Yang
set #1
bqbiol:occursIn Taxonomy Homo sapiens
bqbiol:isVersionOf Gene Ontology arachidonic acid metabolic process
bqbiol:isPartOf KEGG Pathway map00590
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.

Model
Publication ID: 17381237 Submission Date: 09 Apr 2007 19:28:33 UTC Last Modification Date: 05 Jul 2012 14:48:14 UTC Creation Date: 12 Jan 2007 15:06:16 UTC
Mathematical expressions
Reactions
AA production 15-HPETE production 15-HETE production 12-HPETE production
12-HETE production PGH2 production PGE2 production TXA2 production
TXB2 production 5-HPETE production 5-HETE production LTA4 production
LTB4 production 20-OH-LTB4 production 15-LOX upregulation 12-LOX inhibition
TXAS inhibition 5-LOX upregulation LTA4H inhibition TXB2 decay
TXAS inhibition by PGH2 TAX2 decay LTB4 decay LTA4 decay
15-HETE decay 15-HPETE decay 15-LOX decay 5-HETE decay
5-LOX inhibition by x12 5-LOX inhibition by x10 5-LOX inhibition by x2 AA decay
Physical entities
Compartments Species
cell AA 5-HPETE 5-HETE
LTA4 LTB4 w-LTB4
PLA2 15-LOX 12-LOX
COX-2 PGES 15-HPETE
TXAS 5-LOX LTA4H
CYP4F3 PHGPx exo-AA
15-HETE 12-HPETE 12-HETE
PGH2 PGE2 TXA2
TXB2    
Global parameters
lin Kcat(PLA2) Km(PLA2) Kcat(15-LOX)
Km(15-LOX) Kcat(12-LOX) Km(12-LOX) Kcat(COX-2)
Km(COX-2) Kcat(PGES) Km(PGES) Kcat(TXAS)
Km(TXAS) Kcat(5-LOX) Km(5-LOX) Kcat(LTA4H)
Km(LTA4H) Kcat(CYP4F3) Km(CYP4F3) Kcat(PHGPx)
Km(PHGPx) kd2 kd3 kd8
kd9 kd11 kd12 kd13
kd16 ki1 ki2 ki3
ki4 ki5 ki6 ki7
ki8 ki9 ki10 ki11
ki12 ki14 ki15 ki16
ki17 ki18 KI19 KI20
KI21 KI22 KI23 KI24
a24 ks    
Reactions (32)
 
 AA production  → [AA];   {5-HETE} , {LTB4} , {PLA2} , {15-HPETE} , {12-HPETE}
 
 15-HPETE production [AA] ↔ [15-HPETE];   {15-LOX}
 
 15-HETE production [15-HPETE] ↔ [15-HETE];   {PHGPx}
 
 12-HPETE production [AA] ↔ [12-HPETE];   {12-LOX} , {15-HETE}
 
 12-HETE production [12-HPETE] ↔ [12-HETE];   {PHGPx}
 
 PGH2 production [AA] ↔ [PGH2];   {COX-2} , {PGE2}
 
 PGE2 production [PGH2] ↔ [PGE2];   {AA} , {PGES} , {15-HETE}
 
 TXA2 production [PGH2] ↔ [TXA2];   {TXAS}
 
 TXB2 production  → [TXB2];   {TXA2}
 
 5-HPETE production [AA] ↔ [5-HPETE];   {5-HETE} , {15-HETE} , {12-HETE} , {PGE2} , {5-LOX}
 
 5-HETE production [5-HPETE] ↔ [5-HETE];   {PHGPx}
 
 LTA4 production [5-HPETE] ↔ [LTA4];   {5-HETE} , {5-LOX} , {15-HETE} , {12-HETE} , {PGE2}
 
 LTB4 production [LTA4] ↔ [LTB4];   {LTA4H}
 
 20-OH-LTB4 production [LTB4] ↔ [w-LTB4];   {5-HETE} , {CYP4F3} , {12-HETE}
 
 15-LOX upregulation  → [15-LOX];   {PGE2}
 
 12-LOX inhibition [12-LOX] → ;   {15-HPETE}
 
 TXAS inhibition [TXAS] → ;   {15-HPETE}
 
 5-LOX upregulation  → [5-LOX];   {LTB4}
 
 LTA4H inhibition [LTA4H] → ;   {LTA4}
 
 TXB2 decay [TXB2] → ;  
 
 TXAS inhibition by PGH2 [TXAS] → ;   {PGH2}
 
 TAX2 decay [TXA2] → ;  
 
 LTB4 decay [LTB4] → ;  
 
 LTA4 decay [LTA4] → ;  
 
 15-HETE decay [15-HETE] → ;  
 
 15-HPETE decay [15-HPETE] → ;  
 
 15-LOX decay [15-LOX] → ;  
 
 5-HETE decay [5-HETE] → ;  
 
 5-LOX inhibition by x12 [5-LOX] → ;   {LTA4}
 
 5-LOX inhibition by x10 [5-LOX] → ;   {5-HPETE}
 
 5-LOX inhibition by x2 [5-LOX] → ;   {15-HPETE}
 
 AA decay [AA] → ;  
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 AA
Compartment: cell
Initial concentration: 0.0010
 
 5-HPETE
Compartment: cell
Initial concentration: 0.0010
 
 5-HETE
Compartment: cell
Initial concentration: 0.0010
 
 LTA4
Compartment: cell
Initial concentration: 0.0010
 
 LTB4
Compartment: cell
Initial concentration: 0.0010
 
 w-LTB4
Compartment: cell
Initial concentration: 0.0010
 
 PLA2
Compartment: cell
Initial concentration: 1.5
 
 15-LOX
Compartment: cell
Initial concentration: 1.5
 
 12-LOX
Compartment: cell
Initial concentration: 0.5
 
 COX-2
Compartment: cell
Initial concentration: 0.2
 
 PGES
Compartment: cell
Initial concentration: 0.5
 
 15-HPETE
Compartment: cell
Initial concentration: 0.0010
 
 TXAS
Compartment: cell
Initial concentration: 0.5
 
 5-LOX
Compartment: cell
Initial concentration: 5.0
 
 LTA4H
Compartment: cell
Initial concentration: 0.76
 
 CYP4F3
Compartment: cell
Initial concentration: 0.07
 
 PHGPx
Compartment: cell
Initial concentration: 0.8
 
   exo-AA
Compartment: cell
Initial concentration: 0.0
 
 15-HETE
Compartment: cell
Initial concentration: 0.0010
 
 12-HPETE
Compartment: cell
Initial concentration: 0.0010
 
 12-HETE
Compartment: cell
Initial concentration: 0.0010
 
 PGH2
Compartment: cell
Initial concentration: 0.0010
 
 PGE2
Compartment: cell
Initial concentration: 0.0010
 
 TXA2
Compartment: cell
Initial concentration: 0.0010
 
 TXB2
Compartment: cell
Initial concentration: 0.0010
 
Global Parameters (54)
 
   lin
Value: 12.0
Constant
 
 Kcat(PLA2)
Value: 3600.0
Constant
 
 Km(PLA2)
Value: 2600.0
Constant
 
   Kcat(15-LOX)
Value: 1000.0
Constant
 
   Km(15-LOX)
Value: 70.0
Constant
 
   Kcat(12-LOX)
Value: 1000.0
Constant
 
   Km(12-LOX)
Value: 50.0
Constant
 
   Kcat(COX-2)
Value: 1000.0
Constant
 
   Km(COX-2)
Value: 50.0
Constant
 
   Kcat(PGES)
Value: 3000.0
Constant
 
   Km(PGES)
Value: 160.0
Constant
 
   Kcat(TXAS)
Value: 1599.0
Constant
 
   Km(TXAS)
Value: 4.0
Constant
 
   Kcat(5-LOX)
Value: 5000.0
Constant
 
   Km(5-LOX)
Value: 5.0
Constant
 
   Kcat(LTA4H)
Value: 125.0
Constant
 
   Km(LTA4H)
Value: 20.0
Constant
 
   Kcat(CYP4F3)
Value: 150.0
Constant
 
   Km(CYP4F3)
Value: 3.9
Constant
 
   Kcat(PHGPx)
Value: 500.0
Constant
 
   Km(PHGPx)
Value: 70.0
Constant
 
   kd2
Value: 0.05
Constant
 
   kd3
Value: 0.01
Constant
 
   kd8
Value: 0.1
Constant
 
   kd9
Value: 0.0010
Constant
 
   kd11
Value: 0.0010
Constant
 
   kd12
Value: 0.07
Constant
 
   kd13
Value: 0.01
Constant
 
   kd16
Value: 0.01
Constant
 
   ki1
Value: 0.3
Constant
 
   ki2
Value: 30.0
Constant
 
   ki3
Value: 30.0
Constant
 
   ki4
Value: 0.6
Constant
 
   ki5
Value: 0.1
Constant
 
   ki6
Value: 0.01
Constant
 
   ki7
Value: 30.0
Constant
 
   ki8
Value: 4.0
Constant
 
   ki9
Value: 0.175
Constant
 
   ki10
Value: 0.01
Constant
 
   ki11
Value: 15.0
Constant
 
   ki12
Value: 6.3
Constant
 
   ki14
Value: 0.2
Constant
 
   ki15
Value: 0.86
Constant
 
   ki16
Value: 10.0
Constant
 
   ki17
Value: 10.0
Constant
 
   ki18
Value: 10.0
Constant
 
   KI19
Value: 500.0
Constant
 
   KI20
Value: 200.0
Constant
 
   KI21
Value: 500.0
Constant
 
   KI22
Value: 500.0
Constant
 
   KI23
Value: 0.053
Constant
 
   KI24
Value: 2.3E-5
Constant
 
   a24
Value: 0.15
Constant
 
   ks
Value: 500.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000106

Curator's comment: (updated: 23 Mar 2007 20:57:51 GMT)

Figure 2A has been reproduced by SBML ode solver on line.

spacer
spacer