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Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
PKA_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_Unnamed_compartment	reaction21 Unnamed compartment	MassAction	PKA_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): (2.0 * F_B_binding)[s-1.uM-1] reverse rate constant (Kr): (B_kd * F_B_binding)[s-1]
cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment	reaction17 Unnamed compartment	MassAction	cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment
		reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_B_C_Unnamed_compartment) - (Kr * PKA_BB_A_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_B_binding[s-1.uM-1] reverse rate constant (Kr): (F5 * F9 * F_B_binding * B_kd)[s-1]
cAMP_Unnamed_compartment+PKA_2C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment	reaction11 Unnamed compartment	MassAction	cAMP_Unnamed_compartment+PKA_2C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment
		reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_2C_Unnamed_compartment) - (Kr * PKA_B_C2_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): (2.0 * F_B_binding)[s-1.uM-1] reverse rate constant (Kr): (F1 * F2 * B_kd * F_B_binding)[s-1]
PKA_C_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_C_Unnamed_compartment	reaction6 Unnamed compartment	MassAction	PKA_C_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_C_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_C_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_B_binding[s-1.uM-1] reverse rate constant (Kr): (F1 * B_kd * F_B_binding)[s-1]
PKA_BB_A_Unnamed_compartment+C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment	r3 Unnamed compartment	MassAction	PKA_BB_A_Unnamed_compartment+C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_BB_A_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_BB_A_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): (2.0 * C_kr4)[s-1.uM-1] reverse rate constant (Kr): (F5 * F1 * C_kd * C_kr4)[s-1]
C_Unnamed_compartment+PKA_Unnamed_compartmentPKA_C_Unnamed_compartment	reaction5 Unnamed compartment	MassAction	C_Unnamed_compartment+PKA_Unnamed_compartmentPKA_C_Unnamed_compartment
		reaction rate (J): (((Kf * C_Unnamed_compartment) * PKA_Unnamed_compartment) - (Kr * PKA_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): (2.0 * C_kr)[s-1.uM-1] reverse rate constant (Kr): (C_kr * C_kd)[s-1]
cAMP_Unnamed_compartment+PKA_B_Unnamed_compartmentPKA_BB_A_Unnamed_compartment	reaction22 Unnamed compartment	MassAction	cAMP_Unnamed_compartment+PKA_B_Unnamed_compartmentPKA_BB_A_Unnamed_compartment
		reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_B_Unnamed_compartment) - (Kr * PKA_BB_A_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_B_binding[s-1.uM-1] reverse rate constant (Kr): (2.0 * F9 * B_kd * F_B_binding)[s-1]
PKA_C_Unnamed_compartment+C_Unnamed_compartmentPKA_2C_Unnamed_compartment	reaction0 Unnamed compartment	MassAction	PKA_C_Unnamed_compartment+C_Unnamed_compartmentPKA_2C_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_C_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_2C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): C_kr[s-1.uM-1] reverse rate constant (Kr): (2.0 * C_kd2 * C_kr)[s-1]
PKA_B_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C_Unnamed_compartment	r2 Unnamed compartment	MassAction	PKA_B_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_B_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_B_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): C_kr2[s-1.uM-1] reverse rate constant (Kr): (F1 * C_kr2 * C_kd)[s-1]
PKA_B_C_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment	r1 Unnamed compartment	MassAction	PKA_B_C_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_B_C_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_B_C2_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): C_kr2[s-1.uM-1] reverse rate constant (Kr): (F2 * C_kd2 * C_kr2)[s-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
Unnamed compartment	Compartment (+) (-)

Species See in Dashboard
Name	Structure	BioNetGen Definition
PKA_2C_Unnamed_compartment	Unnamed compartment

PKA_BB_A_C_Unnamed_compartment	Unnamed compartment

PKA_BB_A_Unnamed_compartment	Unnamed compartment

cAMP_Unnamed_compartment	Unnamed compartment

PKA_C_Unnamed_compartment	Unnamed compartment

PKA_Unnamed_compartment	Unnamed compartment

PKA_B_C2_Unnamed_compartment	Unnamed compartment

PKA_B_Unnamed_compartment	Unnamed compartment

PKA_B_C_Unnamed_compartment	Unnamed compartment

C_Unnamed_compartment	Unnamed compartment

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications See in Dashboard
Name	Math Type	Annotation
test	Deterministic (ODE) Compartmental

Specifications(Species) - test See in Dashboard
Species	Initial Condition	Diffusion Constant
PKA_2C_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_BB_A_C_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_BB_A_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
cAMP_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_C_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_Unnamed_compartment	0.0125 [uM]	0.0 [um2/s]
PKA_B_C2_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_B_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_B_C_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
C_Unnamed_compartment	5.025 [uM]	0.0 [um2/s]

Specifications(Reaction) - test See in Dashboard
Name	Reaction Mapping
reaction21	included
reaction17	included
reaction11	included
reaction6	included
r3	included
reaction5	included
reaction22	included
reaction0	included
r2	included
r1	included

Simulations - test See in Dashboard
Name	End Time	Output Options
Simulation0	1200.0 [s]	KeepEvery 20 KeepAtMost 6000
Copy of Simulation0	500000.0 [s]	KeepEvery 20 KeepAtMost 6000
Copy of Copy of Simulation0	500000.0 [s]	KeepEvery 20 KeepAtMost 6000
More points free R	500000.0 [s]	KeepEvery 20 KeepAtMost 6000
More points Holo	500000.0 [s]	KeepEvery 20 KeepAtMost 6000

Geometry non-spatial1833399091 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
	Compartmental	Compartment			Unnamed compartment

Global Parameters See in Dashboard
Name	Expression
F_B_binding	0.003175[uM-1.s-1]

B_kd	0.428351[tbd]

B_factor	5.0[tbd]

F_A_binding	0.003[uM-1.s-1]

A_kd	1000.0[tbd]

A_factor	23.0[tbd]

C_kr	0.0023[s-1]

C_kd	3.14E-8[uM]

Vm	0.31[s-1]

Kf_A	0.08[1]

Kr_A	0.012[s-1]

Kf_B	0.082[1]

Kr_B	2.21E-4[s-1]

B1_factor	1.0[tbd]

A1_factor	226.0[tbd]

A2_factor	151.0[tbd]

B2_factor	602.0[tbd]

A2_kd	0.002[tbd]

spots	2.0[uM]

R_A_factor	1.0[tbd]

R_B_factor	1.0[tbd]

F2	1.0[tbd]

F1	1.0[tbd]

F3	439.0[tbd]

F4	30000.0[tbd]

C_kd2	1.96E-5[uM]

C_kr2	0.03[uM-1.s-1]

C_kr3	0.03[uM-1.s-1]

C_kr4	5.0[uM-1.s-1]

C_kr5	0.03[uM-1.s-1]

F7	0.833[tbd]

F9	0.833[tbd]

F5	1.0[tbd]

Name - Boras_PKA_CBD-A_mutant_A-inhibited

BioModel ID - 91147280

Reaction Diagram

Physiology

Applications

Application - test

Global Parameters