ModelBricks - Model Print Page

Name - Boras_PKA-CBD-A

BioModel ID - 91134220

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_A_C_Unnamed_compartment	reaction18 Unnamed compartment	MassAction	cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_A_C_Unnamed_compartment
		reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_B_C_Unnamed_compartment) - (Kr * PKA_B_A_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (2.0 * F3 * A_kd * F_A_binding)[s-1]
PKA_BB_A_C_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_BB_AA_C_Unnamed_compartment	reaction9 Unnamed compartment	MassAction	PKA_BB_A_C_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_BB_AA_C_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_BB_A_C_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_BB_AA_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (F7 * A2_kd * F_A_binding)[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): (2.0 * C_kr2)[s-1.uM-1] reverse rate constant (Kr): (F1 * C_kr2 * C_kd)[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_A_Unnamed_compartmentPKA_BB_A_Unnamed_compartment	reaction22 Unnamed compartment	MassAction	cAMP_Unnamed_compartment+PKA_B_A_Unnamed_compartmentPKA_BB_A_Unnamed_compartment
		reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_B_A_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): (F9 * B_kd * F_B_binding)[s-1]
PKA_BB_A_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_AA_BB_Unnamed_compartment	reaction8 Unnamed compartment	MassAction	PKA_BB_A_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_AA_BB_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_BB_A_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_AA_BB_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (2.0 * A2_kd * F_A_binding)[s-1]
C_Unnamed_compartment+PKA_B_A_C_Unnamed_compartmentPKA_B_A_C2_Unnamed_compartment	reaction1 Unnamed compartment	MassAction	C_Unnamed_compartment+PKA_B_A_C_Unnamed_compartmentPKA_B_A_C2_Unnamed_compartment
		reaction rate (J): (((Kf * C_Unnamed_compartment) * PKA_B_A_C_Unnamed_compartment) - (Kr * PKA_B_A_C2_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): C_kr3[s-1.uM-1] reverse rate constant (Kr): (F2 * F4 * C_kd2 * C_kr3)[s-1]
PKA_B_A_Unnamed_compartment+C_Unnamed_compartmentPKA_B_A_C_Unnamed_compartment	reaction4 Unnamed compartment	MassAction	PKA_B_A_Unnamed_compartment+C_Unnamed_compartmentPKA_B_A_C_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_B_A_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_B_A_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): C_kr3[s-1.uM-1] reverse rate constant (Kr): (F1 * F3 * C_kr3 * C_kd)[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): (2.0 * 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): C_kr4[s-1.uM-1] reverse rate constant (Kr): (F5 * F1 * F3 * C_kd * C_kr4)[s-1]
PKA_B_C2_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_C2_Unnamed_compartment	reaction15 Unnamed compartment	MassAction	PKA_B_C2_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_C2_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_B_C2_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_A_C2_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (F3 * F4 * A_kd * F_A_binding)[s-1]
PKA_B_Unnamed_compartmentPKA_B_B_unnamed_compartment	r0 Unnamed compartment	MassAction	PKA_B_Unnamed_compartmentPKA_B_B_unnamed_compartment
		reaction rate (J): ((Kf * PKA_B_Unnamed_compartment) - (Kr * PKA_B_B_unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_B_binding[s-1] reverse rate constant (Kr): (2.0 * B_kd * F_B_binding)[s-1]
PKA_B_B_unnamed_compartmentPKA_BB_A_Unnamed_compartment	r4 Unnamed compartment	MassAction	PKA_B_B_unnamed_compartmentPKA_BB_A_Unnamed_compartment
		reaction rate (J): ((Kf * PKA_B_B_unnamed_compartment) - (Kr * PKA_BB_A_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): (2.0 * F_A_binding)[s-1] reverse rate constant (Kr): (F9 * A_kd * F_A_binding)[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): (2.0 * F2 * C_kd2 * C_kr2)[s-1]
C_Unnamed_compartment+PKA_AA_BB_Unnamed_compartmentPKA_BB_AA_C_Unnamed_compartment	reaction3 Unnamed compartment	MassAction	C_Unnamed_compartment+PKA_AA_BB_Unnamed_compartmentPKA_BB_AA_C_Unnamed_compartment
		reaction rate (J): (((Kf * C_Unnamed_compartment) * PKA_AA_BB_Unnamed_compartment) - (Kr * PKA_BB_AA_C_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): (2.0 * C_kr5)[s-1.uM-1] reverse rate constant (Kr): (F1 * F5 * C_kd * C_kr5 * F3 * F7)[s-1]
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]
PKA_B_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_Unnamed_compartment	reaction7 Unnamed compartment	MassAction	PKA_B_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_Unnamed_compartment
		reaction rate (J): (((Kf * PKA_B_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_A_Unnamed_compartment))[uM.s-1] forward rate constant (Kf): F_A_binding[s-1.uM-1] reverse rate constant (Kr): (A_kd * F_A_binding)[s-1]
cAMP_Unnamed_compartment+PKA_B_A_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment	reaction17 Unnamed compartment	MassAction	cAMP_Unnamed_compartment+PKA_B_A_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment
		reaction rate (J): (((Kf * cAMP_Unnamed_compartment) * PKA_B_A_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): (F9 * F5 * 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): (F2 * 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]

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_B_A_Unnamed_compartment	Unnamed compartment

PKA_C_Unnamed_compartment	Unnamed compartment

PKA_Unnamed_compartment	Unnamed compartment

PKA_B_C2_Unnamed_compartment	Unnamed compartment

PKA_AA_BB_Unnamed_compartment	Unnamed compartment

PKA_B_Unnamed_compartment	Unnamed compartment

PKA_B_C_Unnamed_compartment	Unnamed compartment

C_Unnamed_compartment	Unnamed compartment

PKA_BB_AA_C_Unnamed_compartment	Unnamed compartment

PKA_B_A_C2_Unnamed_compartment	Unnamed compartment

PKA_B_A_C_Unnamed_compartment	Unnamed compartment

PKA_B_B_unnamed_compartment	Unnamed compartment

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

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

Application - test

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_B_A_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_C_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_Unnamed_compartment	0.011 [uM]	0.0 [um2/s]
PKA_B_C2_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_AA_BB_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	0.02 [uM]	0.0 [um2/s]
PKA_BB_AA_C_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_B_A_C2_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_B_A_C_Unnamed_compartment	0.0 [uM]	0.0 [um2/s]
PKA_B_B_unnamed_compartment	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - test See in Dashboard
Name	Reaction Mapping
reaction18	included
reaction9	included
r2	included
reaction5	included
reaction22	included
reaction8	included
reaction1	included
reaction4	included
reaction6	included
r3	included
reaction15	included
r0	included
r4	included
r1	included
reaction3	included
reaction21	included
reaction7	included
reaction17	included
reaction11	included
reaction0	included

Simulations - test See in Dashboard
Name	End Time	Output Options
Simulation0	1200.0 [s]	KeepEvery 20 KeepAtMost 6000
Copy of Simulation0	5000.0 [s]	KeepEvery 20 KeepAtMost 6000
Copy of Copy of Simulation0	50000.0 [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

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

B_kd	0.428[tbd]

B_factor	5.0[tbd]

F_A_binding	0.003[uM-1.s-1]

A_kd	8.34E-7[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	3.52E-5[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	185.0[tbd]

F4	125000.0[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	0.03[uM-1.s-1]

C_kr5	0.03[uM-1.s-1]

F7	218000.0[tbd]

F9	0.833[tbd]

F5	1.0[tbd]