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Molecule Parameter List for PDGF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| PDGF participated as | Molecule | Sum total of | Enzyme | Substrate of an enzyme | Product of an enzyme | Substrate in Reaction | Product in Reaction |
| No. of occurrences | 1 | 0 | 0 | 0 | 0 | 1 | 0 |
Accession and Pathway Details |
| Accession Name | Accession No. | Accession Type | Pathway Link |
-fig1c | 35 | Network | Shared_Object_MAPK-bistability-fig1c, Sos, PKC, MAPK, PLA2, Ras, PDGFR |
| Model for figure 1c in Bhalla US et al. Science (2002) 297(5583):1018-23. The demo for this figure is available here. This synaptic signaling model is without the MKP-1 feedback, so it is bistable and remains so over long periods. | |||
PDGF acting as a Molecule in MAPK-bistability-fig1c Network
| Name | Accession Name | Pathway Name | Initial Conc. (uM) | Volume (fL) | Buffered | |
| PDGF | -fig1c Accession No. : 35 | PDGFR Pathway No. : 185 | 0 | 1000 | Yes | |
| Platelet-derived growth factor. Heterodimer Mol wt. is approx 30 KDa Deuel et al 1985 Cancer Surv. 4(4):633-53 Conc of 50 ng/ml is close to saturating, and is used by P. Ram (personal communication). Other refs use 65 ng/ml Weise RJ et al 1995 JBC 270(7):3442-3446 A stimulus of 5 min is commonly used. Conversion factor: 1ng/ml = (1e-9/30K)* 1000 Moles/litre = 3e-11M = 3e-5 uM So 50 ng/ml ~ 1.5 nM. | ||||||
PDGF acting as a Substrate in a reaction in MAPK-bistability-fig1c 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 |
| act_PDGFR | -fig1c Accession No. : 35 | PDGFR Pathway No. : 185 | 199.998 (uM^-1 s^-1) | 0.1 (s^-1) | Kd(bf) = 0.0005(uM) | - | Substrate PDGF PDGFR Product L.PDGFR |
| From Heidaran et al JBC268(13):9287 Fig 5. Kd is ~0.5 nM | |||||||