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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 asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000010

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • mkp1_feedback_
    effects
  • 4Network
    Shared_Object_mkp1_feedback_effects Sos PKC 
    MAPK PLA2 Ras 
    PDGFR 
    This is a network involving the MAPK-PKC feedback loop with input from the PDGFR in the synapse. The distinctive feature of this model is that it includes MKP-1 induction by MAPK, and the consequent inhibitory regulation of MAPK and the feedback loop. Lots of interesting dynamics arise from this. This link provides supplementary material for the paper Bhalla US et al. Science (2002) 297(5583):1018-23. In the form of several example simulations and demos for the figures in the paper.

    PDGF acting as a Molecule in  
    mkp1_feedback_effects Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    PDGF
  • mkp1_feedback_
    effects

    Accession No. : 4
  • PDGFR
    Pathway No. : 38
    01000Yes
    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  
    mkp1_feedback_effects 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.
    NameAccession NamePathway NameKfKbKdtauReagents
    act_PDGFR
  • mkp1_feedback_
    effects

    Accession No. : 4
  • PDGFR
    Pathway No. : 38
    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



    Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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