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Molecule Parameter List for PPN

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
PPN participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000022

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
SOCS1_knockout67Pathway
SOCS1_knockout 
This model was taken from the Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6
This model shows the control mechanism of Jak-Stat pathway, here SOCS1 (Suppressor of cytokine signaling-I) was identified as the negative regulator of Jak and STAT signal transduction pathway. This is the knockout version of Jak-Stat pathway in this model the SOCS1 has been knocked out i.e it formation is not shown.
The graphs are almost similar to the graphs as shown in the paper but STAT1n graph has some ambiguities. Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in the simulations.

PPN acting as a Molecule in  
SOCS1_knockout Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
PPNSOCS1_knockout
Accession No. : 67
SOCS1_knockout
Pathway No. : 294
0.060.0016667No
PPX: Unidentified phosphatase in the nucleus PPX = 60nM = 0.06uM Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196

PPN acting as a Substrate in a reaction in  
SOCS1_knockout 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
1PPN_bindingSOCS1_knockout
Accession No. : 67
SOCS1_knockout
Pathway No. : 294
1
(uM^-1 s^-1)
0.2
(s^-1)
Kd(bf) = 0.2(uM)-Substrate
PPN
STAT1n*

Product
PPN-STAT1n*
  Binding of PPN to phosphorylated STAT1n Kf = 1*10e+06 /M/sec = 1/uM/sec Kb = 0.2 /sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196
2PPN_binding[1]SOCS1_knockout
Accession No. : 67
SOCS1_knockout
Pathway No. : 294
1
(uM^-1 s^-1)
0.2
(s^-1)
Kd(bf) = 0.2(uM)-Substrate
PPN
STAT1n*-STAT1n*

Product
  • PPN-STAT1n*-STAT
    1n*

  •   Binding of PPN to phosphorylated STAT1n dimer Kf = 1*10e+06 /M/sec = 1/uM/sec Kb = 0.2 /sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196

    PPN acting as a Product in a reaction in  
    SOCS1_knockout 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
    1
  • STAT1n*_
    dephosphorylatio
    n
  • SOCS1_knockout
    Accession No. : 67
    SOCS1_knockout
    Pathway No. : 294
    0.005
    (s^-1)
    0
    (uM^-1 s^-1)
    --Substrate
    PPN-STAT1n*

    Product
    PPN
    STAT1n
      Nucleoplasmic phosphatase (PPN) dephosphorylates STAT1n Kf = 0.005 /sec Kb = 0 /uM/sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196
    2
  • STAT1n*_
    dephosphorylatio
    n[1]
  • SOCS1_knockout
    Accession No. : 67
    SOCS1_knockout
    Pathway No. : 294
    0.005
    (s^-1)
    0
    (uM^-2 s^-1)
    --Substrate
  • PPN-STAT1n*-STAT
    1n*


    Product
    PPN
    STAT1n
    STAT1n*
  •   Nucleoplasmic phosphatase (PPN) dephosphorylates STAT1n Kf = 0.005 /sec Kb = 0 /uM/sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196



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