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Molecule Parameter List for CycD_Kip1 | 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 | Mammalian_cell_
cycle | 85 | Network |
Growth, CELLDIV, Rb_grp,
IE_GRP, CycB_Grp, Cdc20_Grp,
Cdh1_grp, E2F, CycA_Grp,
CycE_grp, Early_Response_Genes, Delayed_Response_Genes,
CycD_Grp | | This is a fairly complete mass-action reimplementation of the Novak and Tyson mammalian cell cycle model. It is inexact on two counts. First, it replaces many rather abstracted equations with mass action and Michaelis-Menten forms of enzymes. Second, it does not handle the halving of cellular volume at the division point. Within these limitations, the model does most of what the original paper shows including oscillation of the relevant molecules. |
CycD_Kip1 acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CycD_Kip1 | Mammalian_cell_
cycle
Accession No. : 85 | CycD_Grp
Pathway No. : 1081 | 0 | 200 | No |
CycD_Kip1 acting as a Summed Molecule in Mammalian_cell_cycle Network
CycD_Kip1 acting as a Substrate for an Enzyme in Mammalian_cell_cycle Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | CycE /
k6_D_etaE | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 10.0002 | 500 | 4 | explicit E-S complex | Substrate
CycD_Kip1
Product
CycD
degraded
| | | Rate = V6 * [CycD_Kip1]. k3.k1/k2 = rate = k6 * etaE = 50. 6 Apr 2005. Old rates in explicit form were k1 = 500, k2 = 10, k3 = 1. Need to go back to MM form because the above explict rates give a very low Km, ie, lots of E.S complex. k6 = 100, etaE = 0.5, Let Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaE = 500. | | 2 | CycA /
k6_D_etaA | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 10.0002 | 500 | 4 | explicit E-S complex | Substrate
CycD_Kip1
Product
CycD
degraded
| | | k3.k1/k2 = k6.etaA = 100*0.5 = 50 Also k3 << k2. Assume ratio is 10. Let k3 be reasonable, say 1. Then k2 = 10, k1 = 500. 6 April 2005: The above rates are bad because they give a very low Km and too much E.S. complex. So, back to MM: Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaA = 10 * 100 * 0.5 = 500. | | 3 | CycB /
k6_D_etaB | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 9.99992 | 1000 | 4 | explicit E-S complex | Substrate
CycD_Kip1
Product
CycD
degraded
| | | 6 Apr 2005. Earlier used explicit E.S complex form with k1 = 1000, k2 = 10, k3 = 1. This gave low Km and lots of E.S. complex. So shift to MM form: k6 = 100, etaB = 1. Let Km = 10 >> substrate. Then kcat = Km * k6 * etaB = 1000 |
CycD_Kip1 acting as a Substrate in a reaction in Mammalian_cell_cycle 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 | | 1 | k_prime6 | Mammalian_cell_
cycle
Accession No. : 85 | CycD_Grp
Pathway No. : 1081 | 10
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
CycD_Kip1
Product
CycD
degraded
| | 2 | k10_b | Mammalian_cell_
cycle
Accession No. : 85 | CycD_Grp
Pathway No. : 1081 | 5
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
CycD_Kip1
Product
Kip1
degraded
| | | This is another degradation step for CycD, but it happens while the CycD is bound to Kip1. Same rate as k10. |
CycD_Kip1 acting as a Product in a reaction in Mammalian_cell_cycle 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 | | k24 | Mammalian_cell_
cycle
Accession No. : 85 | CycD_Grp
Pathway No. : 1081 | 999.996
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 0.01(uM) | - | Substrate
CycD
Kip1
Product
CycD_Kip1
| | k24 = 1000 k24r = 10 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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