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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 | MAPK_network_
2003 | 50 | Network |
Shared_Object_MAPK_network_2003, PKC, PLA2,
PLCbeta, Gq, MAPK,
Ras, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC | | This is a network model of many pathways present at the neuronal synapse. The network has properties of temporal tuning as well as steady-state computational properties. In its default form the network is bistable.Bhalla US Biophys J. 2004 Aug;87(2):745-53 |
PDE1 acting as a Molecule in MAPK_network_2003 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PDE1 | MAPK_network_
2003
Accession No. : 50 | AC
Pathway No. : 221 | 2 | 1000 | No | | CaM-Dependent PDE. Amount calculated from total rate in brain vs. specific rate. |
PDE1 acting as an Enzyme in MAPK_network_2003 Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | PDE1 /
PDE1
| MAPK_network_
2003
Accession No. : 50 | AC
Pathway No. : 221 | 39.7 | 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 MAPK_network_2003 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 | MAPK_network_
2003
Accession No. : 50 | AC
Pathway No. : 221 | 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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