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Molecule Parameter List for PDE1 | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Ajay_Bhalla_
2004_PKM_Tuning | 76 | Network |
PKC, Shared_Object_Ajay_Bhalla_2004_PKM_tuning, PLA2,
PLCbeta, Gq, MAPK,
Ras, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC, PKM | | This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a. |
PDE1 acting as a Molecule in Ajay_Bhalla_2004_PKM_Tuning Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PDE1 | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | AC
Pathway No. : 327 | 2 | 1.5 | No | | CaM-Dependent PDE. Amount calculated from total rate in brain vs. specific rate. |
PDE1 acting as an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | PDE1 /
PDE1
| Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | AC
Pathway No. : 327 | 39.7006 | 1.667 | 4.0012 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | Rate is 1/6 of the CaM stim form. We'll just reduce all lf k1, k2, k3 so that the Vmax goes down 1/6. |
PDE1 acting as a Substrate in a reaction in Ajay_Bhalla_2004_PKM_Tuning Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | CaM_bind_PDE1 | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | AC
Pathway No. : 327 | 720
(uM^-1 s^-1) | 5
(s^-1) | Kd(bf) = 0.0069(uM) | - | Substrate
CaM-Ca4
PDE1
Product
CaM.PDE1
| | For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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