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Chylek_library.bngl
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# Created by BioNetGen 2.2.6
begin model
begin parameters
NA 6.022e23
celldensity 1e9
Fx 0.02
ECFvol 1/celldensity
simECFvol ECFvol*Fx
Cellvol 1.4e-12
simCellvol Cellvol*Fx
ProteinTot 3e5
SimProteinTot Fx*ProteinTot
LigTot 5e4
SimLigTot Fx*LigTot
lambda_p 1.7e-2
lambda_m 5.4e-2
kfl 0
kxl 1.3/SimProteinTot
krl 1.4e-1
kfRecLyn1 4.2e7/(NA*simCellvol)
krRecLyn1 20
kfRecLyn2 kfRecLyn1
krRecLyn2 0.12
kpLynB1 30
kpLynB2 100
kpLynG1 1
kpLynG2 3
kfLynIn 10
krLynIn 3e-4
kpLynLyn 100
kpFynFyn 100
kfRecSyk 5.1e7/(NA*simCellvol)
krRecSyk 0.13
kpSykSyk0 100
kpSykSykP 200
kpLynSyk1 30
kpLynSyk2 100
kfPagLynSH3 8.4e6/(NA*simCellvol)
krPagLynSH3 30
kfPagLynSH3_2 1e3
kfPagLynSH2 2.5e7/(NA*simCellvol)
kfPagLynSH2_2 1e3
krPagLyn2point 30
kpLynPag 1000
kfCskPag 2.5e4/(NA*simCellvol)
krCskPag 3e-3
kpCskLyn 1000
eff 5
kfRecFyn1 kfRecLyn1
krRecFyn1 krRecLyn1
kfRecFyn2 kfRecLyn2
krRecFyn2 krRecLyn2
kfFynIn kfLynIn
krFynIn krLynIn
kpFynB1 kpLynB1/eff
kpFynB2 kpLynB2/eff
kpFynG1 kpLynG1/eff
kpFynG2 kpLynG2/eff
kpFynSyk1 kpLynSyk1/eff
kpFynSyk2 kpLynSyk2/eff
kfPagFynSH3 kfPagLynSH3
krPagFynSH3 krPagLynSH3
kfPagFynSH3_2 kfPagLynSH3_2
kfPagFynSH2 kfPagLynSH2
kfPagFynSH2_2 kfPagLynSH2_2
krPagFyn2point krPagLyn2point
kpFynPag kpLynPag/eff
kpCskFyn kpCskLyn
kfSykLat kfRecLyn1
krSykLat krRecLyn1
kpSykLat1 kpSykSyk0
kpSykLat2 kpSykSykP
KD_LatPlcg 62e-9
krLatPlcg krRecLyn2
kfLatPlcg (krLatPlcg/KD_LatPlcg)/(NA*simCellvol)
kfPlcgPip2 1e9/(NA*simCellvol)
krPlcgPip2 1
kcPlcgP 3.2e2
kcPlcg0 kcPlcgP/50
krLatGrb2 krRecLyn2
kfLatGrb2 2.5e8/(NA*simCellvol)
KD_Grb2Gab2 8e-6
krGrb2Gab2 1
kfGrb2Gab2 (1/KD_Grb2Gab2)/(NA*simCellvol)
kfFynGab2 kfSykLat
krFynGab2 krSykLat
kpFynGab2 kpFynB1
kfGab2Pi3k kfRecLyn2
krGab2Pi3k krRecLyn2
kfPi3kPip2 kfPlcgPip2
krPi3kPip2 krPlcgPip2
kpPi3k kcPlcgP
kfBtkPip3 1.4e6/(NA*simCellvol)
krBtkPip3 1
kfBtkPlcg kfSykLat
krBtkPlcg krSykLat
kpBtkPlcg kpSykSykP
kfShipRec kfRecLyn2/5
krShipRec krRecLyn2/5
kfShipPip3 kfPlcgPip2
krShipPip3 krPlcgPip2
kdpShipPip3 kcPlcgP
kfShipPip2 kfBtkPip3
krShipPip2 krBtkPip3
kfLatGrap2 6.6e6/(NA*simCellvol)
krLatGrap2 1
kfGrap2Lcp2 9.5e6/(NA*simCellvol)
krGrap2Lcp2 0.06
KD_Lcp2Plcg1 1e-6
krLcp2Plcg1 1
kfLcp2Plcg1 (krLcp2Plcg1/KD_Lcp2Plcg1)/(NA*simCellvol)
kPten 1
kfP5 1
krP5 1
p 1e-3
dp 5
_rateLaw1 100*kfShipRec
_rateLaw2 0.01*kdpShipPip3
_rateLaw3 0.001*kdpShipPip3
ActiveKinase1 0.5*SimProteinTot
ActiveKinase2 0.1*SimProteinTot
ActiveKinase3 0.05*SimProteinTot
kcSyk 100
kcFyn 100
KD1 (79e-9*NA)*simCellvol
KD2 (62e-9*NA)*simCellvol
krSH2 0.12
kfSH2_1 krSH2/KD1
kfSH2_2 krSH2/KD2
kfPH 1.4e6/(NA*simCellvol)
krPH 1
kfSH3 1e6/(NA*simCellvol)
kfSH3_3D 1e6/(NA*simCellvol)
kfSH3_2D 100*kfSH3_3D
krSH3 1
kcBtk 1e-3
kfP 1e9/(NA*simCellvol)
krP 1
kcP 10
kDeg 0.1
kX 5e-3
_rateLaw11 10*kfP
_rateLaw12 5
_rateLaw13 5
_rateLaw14 5
_rateLaw15 5
end parameters
begin molecule types
Sink()
pre()
Pag1(PRS1,Y165_Y183~0~P,PRS2,Y317~0~P,Y386_Y409~0~P)
Grap2(SH2,SH3)
Lcp2(RxxK,PRS)
PI3K(SH2,cat)
Inpp5d(SH2,IPP,C2)
Syk(tSH2,Y346~0~P,cat,Y519_Y520~0~P)
zero()
Lat(Y136~0~P,Y175~0~P)
Lyn(U,SH3,SH2,Y397~0~P,Y508~0~P)
Gab2(PRS,PH,Y441~0~P)
Lig(hap~b~e,hap~b~e)
Plcg1(SH2,SH3,cat,Y783~0~P)
Grb2(SH2,cSH3)
Rec(fab,fab,b_Y218~0~P,b_Y224~0~P,g_Y65_Y76~0~P)
Csk(SH2)
PI(OH3~0~P,OH4~0~P,OH5~0~P,head~0~1)
Fyn(U,SH3,SH2,cat,Y420~0~P,Y531~0~P)
BTK(PH,cat)
end molecule types
begin observables
Molecules PIP3 PI(OH3~P!?,OH4~P,OH5~P,head~1!?)
Molecules PIP2 PI(OH3~0!?,OH4~P,OH5~P,head~1!?)
end observables
begin functions
Replenish() = (kX*PIP2)*(1-(PIP2/SimProteinTot))
end functions
begin species
Lig(hap~b,hap~b) SimLigTot
Rec(b_Y218~0,b_Y224~0,fab,fab,g_Y65_Y76~0) SimProteinTot
Pag1(PRS1,PRS2,Y165_Y183~0,Y317~0,Y386_Y409~0) SimProteinTot
Csk(SH2) SimProteinTot
Lat(Y136~0,Y175~0) SimProteinTot
Grb2(SH2,cSH3) SimProteinTot
Inpp5d(C2,IPP,SH2) SimProteinTot
Grap2(SH2,SH3) SimProteinTot
Lcp2(PRS,RxxK) SimProteinTot
Sink() SimProteinTot
PI3K(SH2,cat) SimProteinTot
PI(OH3~0,OH4~P,OH5~P,head~1) SimProteinTot
pre() SimProteinTot
Lyn(SH2,SH3,U,Y397~0,Y508~0) SimProteinTot
Fyn(SH2,SH3,U,Y420~0,Y531~0,cat) SimProteinTot
Syk(Y346~0,Y519_Y520~0,cat,tSH2) SimProteinTot
Plcg1(SH2,SH3,Y783~0,cat) SimProteinTot
Gab2(PH,PRS,Y441~0) SimProteinTot
BTK(PH,cat) SimProteinTot
end species
begin reaction rules
R1: Lig(hap~b) <-> Lig(hap~e) lambda_p, lambda_m
R2: Lig(hap~e,hap~e) + Rec(fab) -> Lig(hap~e,hap~e!1).Rec(fab!1) kfl
R3: Lig(hap~b,hap~e) + Rec(fab) -> Lig(hap~b,hap~e!1).Rec(fab!1) kfl
R4: Lig(hap~e,hap~e!1).Rec(fab!1) + Rec(fab) -> Lig(hap~e!1,hap~e!2).Rec(fab!2).Rec(fab!1) kxl
R5: Lig(hap~e!1).Rec(fab!1) -> Lig(hap~e) + Rec(fab) krl
R6: Rec(b_Y218~0) + Lyn(U,SH3,SH2) -> Rec(b_Y218~0!1).Lyn(U!1,SH3,SH2) kfRecLyn1
R7: Rec(b_Y218~0!1).Lyn(U!1) -> Rec(b_Y218~0) + Lyn(U) krRecLyn1
R8: Rec(b_Y218~P) + Lyn(U,SH3,SH2) -> Rec(b_Y218~P!1).Lyn(U,SH3,SH2!1) kfRecLyn2
R9: Rec(b_Y218~P!1).Lyn(SH2!1) -> Rec(b_Y218~P) + Lyn(SH2) krRecLyn2
R10: Lyn(U,SH3,SH2,Y508~P) -> Lyn(U,SH3,SH2!1,Y508~P!1) kfLynIn
R11: Lyn(SH2!1,Y508~P!1) -> Lyn(SH2,Y508~P) krLynIn
R12: Lyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218~0) -> Lyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218~P) kpLynB1
R13: Lyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218~0) -> Lyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218~P) kpLynB2
R14: Lyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y224~0) -> Lyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y224~P) kpLynB1
R15: Lyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y224~0) -> Lyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y224~P) kpLynB2
R16: Lyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~0) -> Lyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P) kpLynG1
R17: Lyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~0) -> Lyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P) kpLynG2
R18: Lyn(U!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Lyn(U!4,Y397~0) -> Lyn(U!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Lyn(U!4,Y397~P) kpLynLyn
R19: Lyn(U!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Lyn(SH2!4,Y397~0) -> Lyn(U!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Lyn(SH2!4,Y397~P) kpLynLyn
R20: Lyn(SH2!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Lyn(U!4,Y397~0) -> Lyn(SH2!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Lyn(U!4,Y397~P) kpLynLyn
R21: Lyn(SH2!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Lyn(SH2!4,Y397~0) -> Lyn(SH2!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Lyn(SH2!4,Y397~P) kpLynLyn
R22: Syk(tSH2) + Rec(g_Y65_Y76~P) <-> Syk(tSH2!1).Rec(g_Y65_Y76~P!1) kfRecSyk, krRecSyk
R23: Lyn(U!1,Y397~P).Rec(fab!2,b_Y218~0!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y346~0) -> Lyn(U!1,Y397~P).Rec(fab!2,b_Y218~0!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y346~P) kpLynSyk1
R24: Lyn(SH2!1,Y397~P).Rec(fab!2,b_Y218~P!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y346~0) -> Lyn(SH2!1,Y397~P).Rec(fab!2,b_Y218~P!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y346~P) kpLynSyk2
R25: Syk(tSH2!1,Y519_Y520~0).Rec(fab!2,g_Y65_Y76~P!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y519_Y520~0) -> Syk(tSH2!1,Y519_Y520~0).Rec(fab!2,g_Y65_Y76~P!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y519_Y520~P) kpSykSyk0
R26: Syk(tSH2!1,Y519_Y520~P).Rec(fab!2,g_Y65_Y76~P!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y519_Y520~0) -> Syk(tSH2!1,Y519_Y520~P).Rec(fab!2,g_Y65_Y76~P!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y519_Y520~P) kpSykSykP
R27: Lyn(U,SH3,SH2) + Pag1(PRS2,Y386_Y409) -> Lyn(U,SH3!1,SH2).Pag1(PRS2!1,Y386_Y409) kfPagLynSH3
R28: Lyn(U,SH3,SH2!1).Pag1(PRS2,Y386_Y409~P!1) -> Lyn(U,SH3!1,SH2!2).Pag1(PRS2!1,Y386_Y409~P!2) kfPagLynSH3_2
R29: Lyn(SH3!1,SH2).Pag1(PRS2!1,Y386_Y409) -> Lyn(SH3,SH2) + Pag1(PRS2,Y386_Y409) krPagLynSH3
R30: Lyn(U,SH3,SH2) + Pag1(PRS2,Y386_Y409~P) -> Lyn(U,SH3,SH2!1).Pag1(PRS2,Y386_Y409~P!1) kfPagLynSH2
R31: Lyn(U,SH3!1,SH2).Pag1(PRS2!1,Y386_Y409~P) -> Lyn(U,SH3!1,SH2!2).Pag1(PRS2!1,Y386_Y409~P!2) kfPagLynSH2_2
R32: Lyn(SH3!1,SH2!2).Pag1(PRS2!1,Y386_Y409~P!2) -> Lyn(SH3,SH2) + Pag1(PRS2,Y386_Y409~P) krPagLyn2point
R33: Lyn(SH3!1,Y508,Y397~P).Pag1(PRS2!1,Y386_Y409~0) -> Lyn(SH3!1,Y508,Y397~P).Pag1(PRS2!1,Y386_Y409~P) kpLynPag
R34: Lyn(SH3,SH2!1,Y508,Y397~P).Pag1(Y165_Y183~0,Y386_Y409~P!1) -> Lyn(SH3,SH2!1,Y508,Y397~P).Pag1(Y165_Y183~P,Y386_Y409~P!1) kpLynPag
R35: Lyn(SH3!1,SH2!2,Y508,Y397~P).Pag1(PRS2!1,Y165_Y183~0,Y386_Y409~P!2) -> Lyn(SH3!1,SH2!2,Y508,Y397~P).Pag1(PRS2!1,Y165_Y183~P,Y386_Y409~P!2) kpLynPag
R36: Lyn(SH3!1,SH2,Y508,Y397~P).Pag1(PRS2!1,Y165_Y183~0) -> Lyn(SH3!1,SH2,Y508,Y397~P).Pag1(PRS2!1,Y165_Y183~P) kpLynPag
R37: Lyn(SH2!1,Y508,Y397~P).Pag1(Y317~0,Y386_Y409~P!1) -> Lyn(SH2!1,Y508,Y397~P).Pag1(Y317~P,Y386_Y409~P!1) kpLynPag
R38: Lyn(SH3,SH2!1,Y508,Y397~P).Pag1(Y317~0,Y386_Y409~P!1) -> Lyn(SH3,SH2!1,Y508,Y397~P).Pag1(Y317~P,Y386_Y409~P!1) kpLynPag
R39: Lyn(SH3!1,SH2!2,Y508,Y397~P).Pag1(PRS2!1,Y317~0,Y386_Y409~P!2) -> Lyn(SH3!1,SH2!2,Y508,Y397~P).Pag1(PRS2!1,Y317~P,Y386_Y409~P!2) kpLynPag
R40: Lyn(SH3!1,SH2,Y508,Y397~P).Pag1(PRS2!1,Y317~0) -> Lyn(SH3!1,SH2,Y508,Y397~P).Pag1(PRS2!1,Y317~P) kpLynPag
R41: Csk(SH2) + Pag1(Y317~P) <-> Csk(SH2!1).Pag1(Y317~P!1) kfCskPag, krCskPag
R42: Lyn(SH3,SH2!1,Y508~0).Pag1(Y386_Y409~P!1,Y317~P!2).Csk(SH2!2) -> Lyn(SH3,SH2!1,Y508~P).Pag1(Y386_Y409~P!1,Y317~P!2).Csk(SH2!2) kpCskLyn
R43: Lyn(SH3!1,SH2,Y508~0).Pag1(PRS2!1,Y317~P!2).Csk(SH2!2) -> Lyn(SH3!1,SH2,Y508~P).Pag1(PRS2!1,Y317~P!2).Csk(SH2!2) kpCskLyn
R44: Lyn(SH3!1,SH2!2,Y508~0).Pag1(PRS2!1,Y386_Y409~P!2,Y317~P!3).Csk(SH2!3) -> Lyn(SH3!1,SH2!2,Y508~P).Pag1(PRS2!1,Y386_Y409~P!2,Y317~P!3).Csk(SH2!3) kpCskLyn
R45: Rec(b_Y218~0) + Fyn(U,SH3,SH2) -> Rec(b_Y218~0!1).Fyn(U!1,SH3,SH2) kfRecFyn1
R46: Rec(b_Y218~0!1).Fyn(U!1) -> Rec(b_Y218~0) + Fyn(U) krRecFyn1
R47: Rec(b_Y218~P) + Fyn(U,SH3,SH2) -> Rec(b_Y218~P!1).Fyn(U,SH3,SH2!1) kfRecFyn2
R48: Rec(b_Y218~P!1).Fyn(SH2!1) -> Rec(b_Y218~P) + Fyn(SH2) krRecFyn2
R49: Fyn(U,SH3,SH2,Y531~P) -> Fyn(U,SH3,SH2!1,Y531~P!1) kfFynIn
R50: Fyn(SH2!1,Y531~P!1) -> Fyn(SH2,Y531~P) krFynIn
R51: Fyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218~0) -> Fyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218~P) kpFynB1
R52: Fyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218~0) -> Fyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218~P) kpFynB2
R53: Fyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y224~0) -> Fyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y224~P) kpFynB1
R54: Fyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y224~0) -> Fyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y224~P) kpFynB2
R55: Fyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~0) -> Fyn(U!1).Rec(b_Y218~0!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P) kpFynG1
R56: Fyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~0) -> Fyn(SH2!1).Rec(b_Y218~P!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P) kpFynG2
R57: Fyn(U!1,Y420~P).Rec(fab!2,b_Y218~0!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y346~0) -> Fyn(U!1,Y420~P).Rec(fab!2,b_Y218~0!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y346~P) kpFynSyk1
R58: Fyn(SH2!1,Y420~P).Rec(fab!2,b_Y218~P!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y346~0) -> Fyn(SH2!1,Y420~P).Rec(fab!2,b_Y218~P!1).Lig(hap~e!2,hap~e!3).Rec(fab!3,g_Y65_Y76~P!4).Syk(tSH2!4,Y346~P) kpFynSyk2
R59: Fyn(U!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Fyn(U!4,Y420~0) -> Fyn(U!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Fyn(U!4,Y420~P) kpFynFyn
R60: Fyn(U!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Fyn(SH2!4,Y420~0) -> Fyn(U!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Fyn(SH2!4,Y420~P) kpFynFyn
R61: Fyn(SH2!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Fyn(U!4,Y420~0) -> Fyn(SH2!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Fyn(U!4,Y420~P) kpFynFyn
R62: Fyn(SH2!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Fyn(SH2!4,Y420~0) -> Fyn(SH2!1).Rec(b_Y218!1,fab!2).Lig(hap~e!2,hap~e!3).Rec(fab!3,b_Y218!4).Fyn(SH2!4,Y420~P) kpFynFyn
R63: Fyn(U,SH3,SH2,Y420~P) + Pag1(PRS1,Y165_Y183) -> Fyn(U,SH3!1,SH2,Y420~P).Pag1(PRS1!1,Y165_Y183) kfPagFynSH3
R64: Fyn(U,SH3,SH2!1,Y420~P).Pag1(PRS1,Y165_Y183~P!1) -> Fyn(U,SH3!1,SH2!2,Y420~P).Pag1(PRS1!1,Y165_Y183~P!2) kfPagFynSH3_2
R65: Fyn(SH3!1,SH2,Y420~P).Pag1(PRS1!1,Y165_Y183) -> Fyn(SH3,SH2,Y420~P) + Pag1(PRS1,Y165_Y183) krPagFynSH3
R66: Fyn(U,SH3,SH2,Y420~P) + Pag1(PRS1,Y165_Y183~P) -> Fyn(U,SH3,SH2!1,Y420~P).Pag1(PRS1,Y165_Y183~P!1) kfPagFynSH2
R67: Fyn(U,SH3!1,SH2,Y420~P).Pag1(PRS1!1,Y165_Y183~P) -> Fyn(U,SH3!1,SH2!2,Y420~P).Pag1(PRS1!1,Y165_Y183~P!2) kfPagFynSH2_2
R68: Fyn(SH3!1,SH2!2,Y420~P).Pag1(PRS1!1,Y165_Y183~P!2) -> Fyn(SH3,SH2,Y420~P) + Pag1(PRS1,Y165_Y183~P) krPagFyn2point
R69: Fyn(SH3,SH2!1,Y531,Y420~P).Pag1(Y386_Y409~0,Y165_Y183~P!1) -> Fyn(SH3,SH2!1,Y531,Y420~P).Pag1(Y386_Y409~P,Y165_Y183~P!1) kpFynPag
R70: Fyn(SH3!1,SH2!2,Y531,Y420~P).Pag1(PRS1!1,Y386_Y409~0,Y165_Y183~P!2) -> Fyn(SH3!1,SH2!2,Y531,Y420~P).Pag1(PRS1!1,Y386_Y409~P,Y165_Y183~P!2) kpFynPag
R71: Fyn(SH3!1,SH2,Y531,Y420~P).Pag1(PRS1!1,Y386_Y409~0) -> Fyn(SH3!1,SH2,Y531,Y420~P).Pag1(PRS1!1,Y386_Y409~P) kpFynPag
R72: Fyn(SH3,SH2!1,Y531,Y420~P).Pag1(Y317~0,Y165_Y183~P!1) -> Fyn(SH3,SH2!1,Y531,Y420~P).Pag1(Y317~P,Y165_Y183~P!1) kpFynPag
R73: Fyn(SH3!1,SH2!2,Y531,Y420~P).Pag1(PRS1!1,Y317~0,Y165_Y183~P!2) -> Fyn(SH3!1,SH2!2,Y531,Y420~P).Pag1(PRS1!1,Y317~P,Y165_Y183~P!2) kpFynPag
R74: Fyn(SH3!1,SH2,Y531,Y420~P).Pag1(PRS1!1,Y317~0) -> Fyn(SH3!1,SH2,Y531,Y420~P).Pag1(PRS1!1,Y317~P) kpFynPag
R75: Fyn(SH3,SH2!1,Y531~0).Pag1(Y165_Y183~P!1,Y317~P!2).Csk(SH2!2) -> Fyn(SH3,SH2!1,Y531~P).Pag1(Y165_Y183~P!1,Y317~P!2).Csk(SH2!2) kpCskFyn
R76: Fyn(SH3!1,SH2,Y531~0).Pag1(PRS1!1,Y317~P!2).Csk(SH2!2) -> Fyn(SH3!1,SH2,Y531~P).Pag1(PRS1!1,Y317~P!2).Csk(SH2!2) kpCskFyn
R77: Fyn(SH3!1,SH2!2,Y531~0).Pag1(PRS1!1,Y165_Y183~P!2,Y317~P!3).Csk(SH2!3) -> Fyn(SH3!1,SH2!2,Y531~P).Pag1(PRS1!1,Y165_Y183~P!2,Y317~P!3).Csk(SH2!3) kpCskFyn
R78: Syk(tSH2!+,cat) + Lat(Y175~0) -> Syk(tSH2!+,cat!1).Lat(Y175~0!1) kfSykLat
R79: Syk(cat!1).Lat(Y175~0!1) -> Syk(cat) + Lat(Y175~0) krSykLat
R80: Syk(cat!1,Y519_Y520~P).Lat(Y175~0!1) -> Syk(cat,Y519_Y520~P) + Lat(Y175~P) kpSykLat2
R81: Syk(cat!1,Y519_Y520~0).Lat(Y175~0!1) -> Syk(cat,Y519_Y520~0) + Lat(Y175~P) kpSykLat1
R82: Lat(Y175~P) + Grb2(SH2) <-> Lat(Y175~P!1).Grb2(SH2!1) kfLatGrb2, krLatGrb2
R83: Lat(Y175~P) + Grap2(SH2) <-> Lat(Y175~P!1).Grap2(SH2!1) kfLatGrap2, krLatGrap2
R84: Grap2(SH3) + Lcp2(RxxK) <-> Grap2(SH3!1).Lcp2(RxxK!1) kfGrap2Lcp2, krGrap2Lcp2
R85: Grb2(cSH3) + Gab2(PRS) <-> Grb2(cSH3!1).Gab2(PRS!1) kfGrb2Gab2, krGrb2Gab2
R86: Lcp2(PRS) + Plcg1(SH3) <-> Lcp2(PRS!1).Plcg1(SH3!1) kfLcp2Plcg1, krLcp2Plcg1
R87: Fyn(U!+,SH2,cat) + Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,Y441~0) -> Fyn(U!+,SH2,cat!1).Lat(Y175~P!2).Grb2(SH2!2,cSH3!3).Gab2(PRS!3,Y441~0!1) kfFynGab2
R88: Rec(b_Y218~P!1).Fyn(U,SH2!1,cat) + Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,Y441~0) -> Rec(b_Y218~P!1).Fyn(U,SH2!1,cat!2).Lat(Y175~P!3).Grb2(SH2!3,cSH3!4).Gab2(PRS!4,Y441~0!2) kfFynGab2
R89: Fyn(cat!1).Gab2(Y441~0!1) -> Fyn(cat) + Gab2(Y441~0) krFynGab2
R90: Fyn(cat!1).Gab2(Y441~0!1) -> Fyn(cat) + Gab2(Y441~P) kpFynGab2
R91: Inpp5d(SH2,C2) + Rec(b_Y224~P) -> Inpp5d(SH2!1,C2).Rec(b_Y224~P!1) kfShipRec
R92: Inpp5d(IPP,C2!+) + Rec(b_Y224~P) -> Inpp5d(IPP!1,C2!+).Rec(b_Y224~P!1) _rateLaw1
R93: Inpp5d(SH2!1).Rec(b_Y224~P!1) -> Inpp5d(SH2) + Rec(b_Y224~P) krShipRec
R94: Inpp5d(SH2!+,IPP) + PI(OH3~P,OH4~P,OH5~P,head~1) <-> Inpp5d(SH2!+,IPP!1).PI(OH3~P,OH4~P,OH5~P!1,head~1) kfShipPip3, krShipPip3
R95: Inpp5d(SH2!+,IPP!1).PI(OH3~P,OH4~P,OH5~P!1,head~1) -> Inpp5d(SH2!+,IPP) + PI(OH3~P,OH4~P,OH5~0,head~1) _rateLaw2
R96: Rec(b_Y218~0) -> Rec(b_Y218~P) p
R97: Rec(b_Y218~P) -> Rec(b_Y218~0) dp
R98: Rec(b_Y224~0) -> Rec(b_Y224~P) p
R99: Rec(b_Y224~P) -> Rec(b_Y224~0) dp
R100: Rec(g_Y65_Y76~0) -> Rec(g_Y65_Y76~P) p
R101: Rec(g_Y65_Y76~P) -> Rec(g_Y65_Y76~0) dp
R102: Lyn(Y508~0) -> Lyn(Y508~P) p
R103: Lyn(Y508~P) -> Lyn(Y508~0) dp
R104: Lyn(Y397~0) -> Lyn(Y397~P) p
R105: Lyn(Y397~P) -> Lyn(Y397~0) dp
R106: Fyn(Y531~0) -> Fyn(Y531~P) p
R107: Fyn(Y531~P) -> Fyn(Y531~0) dp
R108: Fyn(Y420~0) -> Fyn(Y420~P) p
R109: Fyn(Y420~P) -> Fyn(Y420~0) dp
R110: Syk(Y346~0) -> Syk(Y346~P) p
R111: Syk(Y346~P) -> Syk(Y346~0) dp
R112: Syk(Y519_Y520~0) -> Syk(Y519_Y520~P) p
R113: Syk(Y519_Y520~P) -> Syk(Y519_Y520~0) dp
R114: Pag1(Y317~0) -> Pag1(Y317~P) p
R115: Pag1(Y317~P) -> Pag1(Y317~0) dp
R116: Pag1(Y165_Y183~0) -> Pag1(Y165_Y183~P) p
R117: Pag1(Y165_Y183~P) -> Pag1(Y165_Y183~0) dp
R118: Pag1(Y386_Y409~0) -> Pag1(Y386_Y409~P) p
R119: Pag1(Y386_Y409~P) -> Pag1(Y386_Y409~0) dp
R120: Gab2(Y441~0) -> Gab2(Y441~P) p
R121: Gab2(Y441~P) -> Gab2(Y441~0) dp
R122: Lat(Y136~0) -> Lat(Y136~P) p
R123: Lat(Y136~P) -> Lat(Y136~0) dp
R124: Lat(Y175~0) -> Lat(Y175~P) p
R125: Lat(Y175~P) -> Lat(Y175~0) dp
R126: Plcg1(Y783~0) -> Plcg1(Y783~P) p
R127: Plcg1(Y783~P) -> Plcg1(Y783~0) dp
R128: Lat(Y136~0) + Syk(cat) <-> Lat(Y136~0!1).Syk(cat!1) kfSH3, krSH3
R129: Lat(Y136~0!1).Syk(cat!1) -> Lat(Y136~P) + Syk(cat) kcSyk
R130: Lat(Y175~0) + Syk(cat) <-> Lat(Y175~0!1).Syk(cat!1) kfSH3, krSH3
R131: Lat(Y175~0!1).Syk(cat!1) -> Lat(Y175~P) + Syk(cat) kcSyk
R132: Lat(Y136~P) + Plcg1(SH2) <-> Lat(Y136~P!1).Plcg1(SH2!1) kfSH2_2, krSH2
R133: Lat(Y175~P) + Grb2(SH2) <-> Lat(Y175~P!1).Grb2(SH2!1) kfSH2_1, krSH2
R134: Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,PH,Y441~0) + Fyn(cat) -> Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,PH,Y441~0!3).Fyn(cat!3) kfSH3
R135: Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,PH!+,Y441~0) + Fyn(cat) -> Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,PH!+,Y441~0!3).Fyn(cat!3) kfSH3
R136: Gab2(PRS,PH!+,Y441~0) + Fyn(cat) -> Gab2(PRS,PH!+,Y441~0!1).Fyn(cat!1) kfSH3
R137: Grb2(SH2,cSH3!1).Gab2(PRS!1,PH!+,Y441~0) + Fyn(cat) -> Grb2(SH2,cSH3!1).Gab2(PRS!1,PH!+,Y441~0!2).Fyn(cat!2) kfSH3
R138: Gab2(Y441~0!1).Fyn(cat!1) -> Gab2(Y441~0) + Fyn(cat) krSH3
R139: Gab2(Y441~0!1).Fyn(cat!1) -> Gab2(Y441~P) + Fyn(cat) kcFyn
R140: Grb2(SH2,cSH3) + Gab2(PRS,PH!+) -> Grb2(SH2,cSH3!1).Gab2(PRS!1,PH!+) kfSH3_3D
R141: Grb2(SH2!+,cSH3) + Gab2(PRS,PH) -> Grb2(SH2!+,cSH3!1).Gab2(PRS!1,PH) kfSH3_3D
R142: Grb2(SH2,cSH3) + Gab2(PRS,PH) -> Grb2(SH2,cSH3!1).Gab2(PRS!1,PH) kfSH3_3D
R143: Grb2(SH2!+,cSH3) + Gab2(PRS,PH!+) -> Grb2(SH2!+,cSH3!1).Gab2(PRS!1,PH!+) kfSH3_2D
R144: Grb2(cSH3!1).Gab2(PRS!1) -> Grb2(cSH3) + Gab2(PRS) krSH3
R145: Gab2(Y441~P) + PI3K(SH2) <-> Gab2(Y441~P!1).PI3K(SH2!1) kfSH2_1, krSH2
R146: Gab2(PH) + PI(OH3~P,OH4~P,OH5~P,head~1) <-> Gab2(PH!1).PI(OH3~P,OH4~P,OH5~P,head~1!1) kfPH, krPH
R147: Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,PH,Y441~P!3).PI3K(SH2!3,cat) + PI(OH3~0,OH4~P,OH5~P,head~1) -> Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,PH,Y441~P!3).PI3K(SH2!3,cat!4).PI(OH3~0!4,OH4~P,OH5~P,head~1) kfP
R148: Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,PH!+,Y441~P!3).PI3K(SH2!3,cat) + PI(OH3~0,OH4~P,OH5~P,head~1) -> Lat(Y175~P!1).Grb2(SH2!1,cSH3!2).Gab2(PRS!2,PH!+,Y441~P!3).PI3K(SH2!3,cat!4).PI(OH3~0!4,OH4~P,OH5~P,head~1) kfP
R149: Gab2(PRS,PH!+,Y441~P!1).PI3K(SH2!1,cat) + PI(OH3~0,OH4~P,OH5~P,head~1) -> Gab2(PRS,PH!+,Y441~P!1).PI3K(SH2!1,cat!2).PI(OH3~0!2,OH4~P,OH5~P,head~1) kfP
R150: Grb2(SH2,cSH3!1).Gab2(PRS!1,PH!+,Y441~P!2).PI3K(SH2!2,cat) + PI(OH3~0,OH4~P,OH5~P,head~1) -> Grb2(SH2,cSH3!1).Gab2(PRS!1,PH!+,Y441~P!2).PI3K(SH2!2,cat!3).PI(OH3~0!3,OH4~P,OH5~P,head~1) kfP
R151: PI3K(cat!1).PI(OH3~0!1,OH4~P,OH5~P,head~1) -> PI3K(cat) + PI(OH3~0,OH4~P,OH5~P,head~1) krP
R152: PI3K(cat!1).PI(OH3~0!1,OH4~P,OH5~P,head~1) -> PI3K(cat) + PI(OH3~P,OH4~P,OH5~P,head~1) kcP
R153: PI(OH3~P,OH4~P,OH5~P,head~1) + BTK(PH) <-> PI(OH3~P,OH4~P,OH5~P,head~1!1).BTK(PH!1) kfPH, krPH
R154: BTK(PH!+,cat) + Plcg1(SH2!+,Y783~0) -> BTK(PH!+,cat!1).Plcg1(SH2!+,Y783~0!1) kfSH3
R155: BTK(cat!1).Plcg1(Y783~0!1) -> BTK(cat) + Plcg1(Y783~0) krSH3
R156: BTK(cat!1).Plcg1(Y783~0!1) -> BTK(cat) + Plcg1(Y783~P) kcSyk
R157: Plcg1(cat,SH2!+,Y783~P) + PI(OH3~0,OH4~P,OH5~P,head~1) -> Plcg1(cat!1,SH2!+,Y783~P).PI(OH3~0,OH4~P,OH5~P,head~1!1) _rateLaw11
R158: Plcg1(cat!1).PI(head~1!1) -> Plcg1(cat) + PI(head~1) krP
R159: Plcg1(cat!1).PI(head~1!1) -> Plcg1(cat) + PI(head~0) kcP
R160: PI(OH3~0,OH4~P,OH5~P,head~0) -> zero() kDeg
R161: PI(OH3~P,OH4~P,OH5~P,head~1) -> PI(OH3~0,OH4~P,OH5~P,head~1) kPten
R162: pre() -> pre() + PI(OH3~0,OH4~P,OH5~P,head~1) Replenish()
end reaction rules
end model
# 1. Run with this line uncommented to generate the opts file. Copy this file to the top level project folder
# (if using RuleBender).
#visualize({type=>"opts"})
# 2. Now uncomment the next line to use the opts file.
#visualize({type=>"regulatory",groups=>1,collapse=>1,opts=>"../../../Chylek_library_opts.txt",doNotUseContextWhenGrouping=>1})