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Contents |
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* Residue conservation analysis
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Enzyme class:
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Chains A, C:
E.C.2.7.11.22
- Cyclin-dependent kinase.
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Reaction:
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ATP + a protein = ADP + a phosphoprotein
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ATP
Bound ligand (Het Group name = )
corresponds exactly
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+
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protein
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=
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ADP
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+
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phosphoprotein
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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cyclin-dependent protein kinase holoenzyme complex
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15 terms
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Biological process
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regulation of gene silencing
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34 terms
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Biochemical function
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nucleotide binding
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13 terms
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DOI no:
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Nature
376:313-320
(1995)
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PubMed id:
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Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex.
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P.D.Jeffrey,
A.A.Russo,
K.Polyak,
E.Gibbs,
J.Hurwitz,
J.Massagué,
N.P.Pavletich.
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ABSTRACT
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The crystal structure of the human cyclinA-cyclin-dependent kinase2 (CDK2)-ATP
complex has been determined at 2.3 A resolution. CyclinA binds to one side of
CDK2's catalytic cleft, inducing large conformational changes in its PSTAIRE
helix and T-loop. These changes activate the kinase by realigning active site
residues and relieving the steric blockade at the entrance of the catalytic
cleft.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Stein,
A.Céol,
and
P.Aloy
(2011).
3did: identification and classification of domain-based interactions of known three-dimensional structure.
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Nucleic Acids Res, 39,
D718-D723.
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B.M.Filippi,
P.de Los Heros,
Y.Mehellou,
I.Navratilova,
R.Gourlay,
M.Deak,
L.Plater,
R.Toth,
E.Zeqiraj,
and
D.R.Alessi
(2011).
MO25 is a master regulator of SPAK/OSR1 and MST3/MST4/YSK1 protein kinases.
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EMBO J, 30,
1730-1741.
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G.Xu,
Y.C.Lo,
Q.Li,
G.Napolitano,
X.Wu,
X.Jiang,
M.Dreano,
M.Karin,
and
H.Wu
(2011).
Crystal structure of inhibitor of κB kinase β.
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| |
Nature, 472,
325-330.
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PDB codes:
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J.D.Sadowsky,
M.A.Burlingame,
D.W.Wolan,
C.L.McClendon,
M.P.Jacobson,
and
J.A.Wells
(2011).
Turning a protein kinase on or off from a single allosteric site via disulfide trapping.
|
| |
Proc Natl Acad Sci U S A, 108,
6056-6061.
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PDB codes:
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J.Węsierska-Gądek,
M.Maurer,
N.Zulehner,
and
O.Komina
(2011).
Whether to target single or multiple CDKs for therapy? That is the question.
|
| |
J Cell Physiol, 226,
341-349.
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|
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|
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L.P.Albou,
O.Poch,
and
D.Moras
(2011).
M-ORBIS: mapping of molecular binding sites and surfaces.
|
| |
Nucleic Acids Res, 39,
30-43.
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|
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|
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L.Zhang,
H.Zhu,
Q.Wang,
H.Fang,
W.Xu,
and
M.Li
(2011).
Homology modeling, molecular dynamic simulation and docking studies of cyclin dependent kinase 1.
|
| |
J Mol Model, 17,
219-226.
|
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|
|
|
M.Mustafa,
A.Mirza,
and
N.Kannan
(2011).
Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: a molecular dynamics study.
|
| |
Proteins, 79,
99.
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|
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|
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|
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N.Jura,
X.Zhang,
N.F.Endres,
M.A.Seeliger,
T.Schindler,
and
J.Kuriyan
(2011).
Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms.
|
| |
Mol Cell, 42,
9.
|
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|
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S.S.Taylor,
and
A.P.Kornev
(2011).
Protein kinases: evolution of dynamic regulatory proteins.
|
| |
Trends Biochem Sci, 36,
65-77.
|
|
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|
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|
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S.Y.Lu,
Y.J.Jiang,
J.W.Zou,
and
T.X.Wu
(2011).
Dissection of the difference between the group I metal ions in inhibiting GSK3β: a computational study.
|
| |
Phys Chem Chem Phys, 13,
7014-7023.
|
|
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|
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|
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A.Cardone,
R.W.Albers,
R.D.Sriram,
and
H.C.Pant
(2010).
Evaluation of the interaction of cyclin-dependent kinase 5 with activator p25 and with p25-derived inhibitor CIP.
|
| |
J Comput Biol, 17,
707-721.
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B.Zhang,
Z.C.Su,
T.E.Tay,
and
V.B.Tan
(2010).
Mechanism of CDK5 activation revealed by steered molecular dynamics simulations and energy calculations.
|
| |
J Mol Model, 16,
1159-1168.
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C.V.Kuny,
K.Chinchilla,
M.R.Culbertson,
and
R.F.Kalejta
(2010).
Cyclin-dependent kinase-like function is shared by the beta- and gamma- subset of the conserved herpesvirus protein kinases.
|
| |
PLoS Pathog, 6,
0.
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D.Liu,
and
R.L.Finley
(2010).
Cyclin Y is a novel conserved cyclin essential for development in Drosophila.
|
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Genetics, 184,
1025-1035.
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D.Tobi
(2010).
Designing coarse grained-and atom based-potentials for protein-protein docking.
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BMC Struct Biol, 10,
40.
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E.Zeqiraj,
and
D.M.van Aalten
(2010).
Pseudokinases-remnants of evolution or key allosteric regulators?
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Curr Opin Struct Biol, 20,
772-781.
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F.K.Yousafzai,
N.Al-Kaff,
and
G.Moore
(2010).
The molecular features of chromosome pairing at meiosis: the polyploid challenge using wheat as a reference.
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Funct Integr Genomics, 10,
147-156.
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F.K.Yousafzai,
N.Al-Kaff,
and
G.Moore
(2010).
Structural and functional relationship between the Ph1 locus protein 5B2 in wheat and CDK2 in mammals.
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Funct Integr Genomics, 10,
157-166.
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G.Pascreau,
F.Eckerdt,
M.E.Churchill,
and
J.L.Maller
(2010).
Discovery of a distinct domain in cyclin A sufficient for centrosomal localization independently of Cdk binding.
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| |
Proc Natl Acad Sci U S A, 107,
2932-2937.
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I.Buch,
D.Fishelovitch,
N.London,
B.Raveh,
H.J.Wolfson,
and
R.Nussinov
(2010).
Allosteric regulation of glycogen synthase kinase 3β: a theoretical study.
|
| |
Biochemistry, 49,
10890-10901.
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J.H.Bae,
and
J.Schlessinger
(2010).
Asymmetric tyrosine kinase arrangements in activation or autophosphorylation of receptor tyrosine kinases.
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Mol Cells, 29,
443-448.
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J.M.Enserink,
and
R.D.Kolodner
(2010).
An overview of Cdk1-controlled targets and processes.
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Cell Div, 5,
11.
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K.A.Merrick,
and
R.P.Fisher
(2010).
Putting one step before the other: distinct activation pathways for Cdk1 and Cdk2 bring order to the mammalian cell cycle.
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Cell Cycle, 9,
706-714.
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K.Engels,
C.Beyer,
M.L.Suárez Fernández,
F.Bender,
M.Gassel,
G.Unden,
R.J.Marhöfer,
J.C.Mottram,
and
P.M.Selzer
(2010).
Inhibition of Eimeria tenella CDK-related kinase 2: From target identification to lead compounds.
|
| |
ChemMedChem, 5,
1259-1271.
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L.Kurzawa,
and
M.C.Morris
(2010).
Cell-cycle markers and biosensors.
|
| |
Chembiochem, 11,
1037-1047.
|
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M.Rabiller,
M.Getlik,
S.Klüter,
A.Richters,
S.Tückmantel,
J.R.Simard,
and
D.Rauh
(2010).
Proteus in the world of proteins: conformational changes in protein kinases.
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Arch Pharm (Weinheim), 343,
193-206.
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P.Ranjitkar,
A.M.Brock,
and
D.J.Maly
(2010).
Affinity reagents that target a specific inactive form of protein kinases.
|
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Chem Biol, 17,
195-206.
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Y.W.Ng,
D.Raghunathan,
P.M.Chan,
Y.Baskaran,
D.J.Smith,
C.H.Lee,
C.Verma,
and
E.Manser
(2010).
Why an A-loop phospho-mimetic fails to activate PAK1: understanding an inaccessible kinase state by molecular dynamics simulations.
|
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Structure, 18,
879-890.
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A.Gárriz,
H.Qiu,
M.Dey,
E.J.Seo,
T.E.Dever,
and
A.G.Hinnebusch
(2009).
A network of hydrophobic residues impeding helix alphaC rotation maintains latency of kinase Gcn2, which phosphorylates the alpha subunit of translation initiation factor 2.
|
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Mol Cell Biol, 29,
1592-1607.
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A.Papakyriakou,
D.Vourloumis,
F.Tzortzatou-Stathopoulou,
and
M.Karpusas
(2009).
Conformational dynamics of the EGFR kinase domain reveals structural features involved in activation.
|
| |
Proteins, 76,
375-386.
|
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C.Hyeon,
P.A.Jennings,
J.A.Adams,
and
J.N.Onuchic
(2009).
Ligand-induced global transitions in the catalytic domain of protein kinase A.
|
| |
Proc Natl Acad Sci U S A, 106,
3023-3028.
|
|
|
|
|
|
|
D.Raffa,
B.Maggio,
S.Cascioferro,
M.V.Raimondi,
G.Daidone,
S.Plescia,
D.Schillaci,
M.G.Cusimano,
L.Titone,
C.Colomba,
and
M.Tolomeo
(2009).
N-(indazolyl)benzamido derivatives as CDK1 inhibitors: design, synthesis, biological activity, and molecular docking studies.
|
| |
Arch Pharm (Weinheim), 342,
265-273.
|
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|
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D.W.Pettigrew
(2009).
Oligomeric interactions provide alternatives to direct steric modes of control of sugar kinase/actin/hsp70 superfamily functions by heterotropic allosteric effectors: inhibition of E. coli glycerol kinase.
|
| |
Arch Biochem Biophys, 492,
29-39.
|
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E.K.Schrader,
K.G.Harstad,
and
A.Matouschek
(2009).
Targeting proteins for degradation.
|
| |
Nat Chem Biol, 5,
815-822.
|
|
|
|
|
|
|
E.Zeqiraj,
B.M.Filippi,
S.Goldie,
I.Navratilova,
J.Boudeau,
M.Deak,
D.R.Alessi,
and
D.M.van Aalten
(2009).
ATP and MO25alpha regulate the conformational state of the STRADalpha pseudokinase and activation of the LKB1 tumour suppressor.
|
| |
PLoS Biol, 7,
e1000126.
|
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PDB code:
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G.Kontopidis,
M.J.Andrews,
C.McInnes,
A.Plater,
L.Innes,
S.Renachowski,
A.Cowan,
and
P.M.Fischer
(2009).
Truncation and optimisation of peptide inhibitors of cyclin-dependent kinase 2-cyclin a through structure-guided design.
|
| |
ChemMedChem, 4,
1120-1128.
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PDB codes:
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I.Westwood,
D.M.Cheary,
J.E.Baxter,
M.W.Richards,
R.L.van Montfort,
A.M.Fry,
and
R.Bayliss
(2009).
Insights into the conformational variability and regulation of human Nek2 kinase.
|
| |
J Mol Biol, 386,
476-485.
|
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PDB codes:
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J.Baselga,
and
S.M.Swain
(2009).
Novel anticancer targets: revisiting ERBB2 and discovering ERBB3.
|
| |
Nat Rev Cancer, 9,
463-475.
|
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J.Wesierska-Gadek,
and
V.Krystof
(2009).
Selective cyclin-dependent kinase inhibitors discriminating between cell cycle and transcriptional kinases: future reality or utopia?
|
| |
Ann N Y Acad Sci, 1171,
228-241.
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K.J.Thomas,
and
M.R.Cookson
(2009).
The role of PTEN-induced kinase 1 in mitochondrial dysfunction and dynamics.
|
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Int J Biochem Cell Biol, 41,
2025-2035.
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K.Streckfuss-Bömeke,
F.Schulze,
B.Herzog,
E.Scholz,
and
G.H.Braus
(2009).
Degradation of Saccharomyces cerevisiae transcription factor Gcn4 requires a C-terminal nuclear localization signal in the cyclin Pcl5.
|
| |
Eukaryot Cell, 8,
496-510.
|
|
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|
|
|
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L.M.Elphick,
S.E.Lee,
E.S.Child,
A.Prasad,
C.Pignocchi,
S.Thibaudeau,
A.A.Anderson,
L.Bonnac,
V.Gouverneur,
and
D.J.Mann
(2009).
A quantitative comparison of wild-type and gatekeeper mutant cdk2 for chemical genetic studies with ATP analogues.
|
| |
Chembiochem, 10,
1519-1526.
|
|
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M.Malakhova,
I.Kurinov,
K.Liu,
D.Zheng,
I.D'Angelo,
J.H.Shim,
V.Steinman,
A.M.Bode,
and
Z.Dong
(2009).
Structural diversity of the active N-terminal kinase domain of p90 ribosomal S6 kinase 2.
|
| |
PLoS One, 4,
e8044.
|
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PDB code:
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M.Orzáez,
A.Gortat,
L.Mondragón,
O.Bachs,
and
E.Pérez-Payá
(2009).
ATP-noncompetitive inhibitors of CDK-cyclin complexes.
|
| |
ChemMedChem, 4,
19-24.
|
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N.Jura,
Y.Shan,
X.Cao,
D.E.Shaw,
and
J.Kuriyan
(2009).
Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3.
|
| |
Proc Natl Acad Sci U S A, 106,
21608-21613.
|
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PDB code:
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P.Corsino,
N.Horenstein,
D.Ostrov,
T.Rowe,
M.Law,
A.Barrett,
G.Aslanidi,
W.D.Cress,
and
B.Law
(2009).
A novel class of cyclin-dependent kinase inhibitors identified by molecular docking act through a unique mechanism.
|
| |
J Biol Chem, 284,
29945-29955.
|
|
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|
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|
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P.J.Day,
A.Cleasby,
I.J.Tickle,
M.O'Reilly,
J.E.Coyle,
F.P.Holding,
R.L.McMenamin,
J.Yon,
R.Chopra,
C.Lengauer,
and
H.Jhoti
(2009).
Crystal structure of human CDK4 in complex with a D-type cyclin.
|
| |
Proc Natl Acad Sci U S A, 106,
4166-4170.
|
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PDB codes:
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P.M.Price,
R.L.Safirstein,
and
J.Megyesi
(2009).
The cell cycle and acute kidney injury.
|
| |
Kidney Int, 76,
604-613.
|
|
|
|
|
|
|
S.Prakash,
T.Inobe,
A.J.Hatch,
and
A.Matouschek
(2009).
Substrate selection by the proteasome during degradation of protein complexes.
|
| |
Nat Chem Biol, 5,
29-36.
|
|
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|
|
|
|
T.Takaki,
A.Echalier,
N.R.Brown,
T.Hunt,
J.A.Endicott,
and
M.E.Noble
(2009).
The structure of CDK4/cyclin D3 has implications for models of CDK activation.
|
| |
Proc Natl Acad Sci U S A, 106,
4171-4176.
|
|
|
PDB code:
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V.Calleja,
M.Laguerre,
and
B.Larijani
(2009).
3-D structure and dynamics of protein kinase B-new mechanism for the allosteric regulation of an AGC kinase.
|
| |
J Chem Biol, 2,
11-25.
|
|
|
|
|
|
|
W.Qiu,
A.Wernimont,
K.Tang,
S.Taylor,
V.Lunin,
M.Schapira,
S.Fentress,
R.Hui,
and
L.D.Sibley
(2009).
Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii.
|
| |
EMBO J, 28,
969-979.
|
|
|
PDB codes:
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|
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|
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X.Huang,
P.Finerty,
J.R.Walker,
C.Butler-Cole,
M.Vedadi,
M.Schapira,
S.A.Parker,
B.E.Turk,
D.A.Thompson,
and
S.Dhe-Paganon
(2009).
Structural insights into the inhibited states of the Mer receptor tyrosine kinase.
|
| |
J Struct Biol, 165,
88-96.
|
|
|
PDB codes:
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|
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|
|
Y.J.Xu,
and
T.J.Kelly
(2009).
Autoinhibition and autoactivation of the DNA replication checkpoint kinase cds1.
|
| |
J Biol Chem, 284,
16016-16027.
|
|
|
|
|
|
|
A.Degterev,
J.Hitomi,
M.Germscheid,
I.L.Ch'en,
O.Korkina,
X.Teng,
D.Abbott,
G.D.Cuny,
C.Yuan,
G.Wagner,
S.M.Hedrick,
S.A.Gerber,
A.Lugovskoy,
and
J.Yuan
(2008).
Identification of RIP1 kinase as a specific cellular target of necrostatins.
|
| |
Nat Chem Biol, 4,
313-321.
|
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|
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A.J.Hume,
J.S.Finkel,
J.P.Kamil,
D.M.Coen,
M.R.Culbertson,
and
R.F.Kalejta
(2008).
Phosphorylation of retinoblastoma protein by viral protein with cyclin-dependent kinase function.
|
| |
Science, 320,
797-799.
|
|
|
|
|
|
|
A.R.Mattoo,
A.Arora,
S.Maiti,
and
Y.Singh
(2008).
Identification, characterization and activation mechanism of a tyrosine kinase of Bacillus anthracis.
|
| |
FEBS J, 275,
6237-6247.
|
|
|
|
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|
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A.Torkamani,
N.Kannan,
S.S.Taylor,
and
N.J.Schork
(2008).
Congenital disease SNPs target lineage specific structural elements in protein kinases.
|
| |
Proc Natl Acad Sci U S A, 105,
9011-9016.
|
|
|
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|
|
C.Denicourt,
P.Legault,
F.A.McNabb,
and
E.Rassart
(2008).
Human and mouse cyclin D2 splice variants: transforming activity and subcellular localization.
|
| |
Oncogene, 27,
1253-1262.
|
|
|
|
|
|
|
C.Qiu,
M.K.Tarrant,
S.H.Choi,
A.Sathyamurthy,
R.Bose,
S.Banjade,
A.Pal,
W.G.Bornmann,
M.A.Lemmon,
P.A.Cole,
and
D.J.Leahy
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PDB code:
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D.J.Wolgemuth,
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Structure, 12,
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PDB codes:
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D.Wu,
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Nature, 425,
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PDB codes:
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Structure, 11,
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PDB code:
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PDB code:
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T.Goda,
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PDB code:
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