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Contents |
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* Residue conservation analysis
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PDB id:
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Transferase
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Title:
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Structural basis for the auto-inhibition of c-abl tyrosine kinase
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Structure:
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Proto-oncogene tyrosine-protein kinase. Chain: a, b. Fragment: n-terminal 531 residues (myr-sh3-sh2-kinase domain). Engineered: yes. Mutation: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: abl. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
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Resolution:
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3.42Å
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R-factor:
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0.306
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R-free:
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0.315
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Authors:
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B.Nagar,O.Hantschel,M.A.Young,K.Scheffzek,D.Veach,W.Bornmann, B.Clarkson,G.Superti-Furga,J.Kuriyan
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Key ref:
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B.Nagar
et al.
(2003).
Structural basis for the autoinhibition of c-Abl tyrosine kinase.
Cell,
112,
859-871.
PubMed id:
DOI:
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Date:
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06-Mar-03
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Release date:
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08-Apr-03
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PROCHECK
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Headers
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References
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Enzyme class:
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Chains A, B:
E.C.2.7.10.2
- non-specific protein-tyrosine kinase.
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Reaction:
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L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H+
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L-tyrosyl-[protein]
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+
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ATP
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=
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O-phospho-L-tyrosyl-[protein]
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+
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ADP
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Cell
112:859-871
(2003)
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PubMed id:
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Structural basis for the autoinhibition of c-Abl tyrosine kinase.
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B.Nagar,
O.Hantschel,
M.A.Young,
K.Scheffzek,
D.Veach,
W.Bornmann,
B.Clarkson,
G.Superti-Furga,
J.Kuriyan.
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ABSTRACT
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c-Abl is normally regulated by an autoinhibitory mechanism, the disruption of
which leads to chronic myelogenous leukemia. The details of this mechanism have
been elusive because c-Abl lacks a phosphotyrosine residue that triggers the
assembly of the autoinhibited form of the closely related Src kinases by
internally engaging the SH2 domain. Crystal structures of c-Abl show that the
N-terminal myristoyl modification of c-Abl 1b binds to the kinase domain and
induces conformational changes that allow the SH2 and SH3 domains to dock onto
it. Autoinhibited c-Abl forms an assembly that is strikingly similar to that of
inactive Src kinases but with specific differences that explain the differential
ability of the drug STI-571/Gleevec/imatinib (STI-571) to inhibit the catalytic
activity of Abl, but not that of c-Src.
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Selected figure(s)
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Figure 2.
Figure 2. Structure of Assembled c-Abl(A) Ribbon and
surface representations of c-Abl (Structure C).(B) Superposition
of the structure of c-Src (red; PDB code 2SRC) onto the SH3 and
SH2 domains (residues 83–233) of Abl^46–534 (Structure C;
green).
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Figure 4.
Figure 4. SH2 Gating MechanismRibbon and surface
representation of Abl^46–534 (Structure C) depicting the clash
that occurs between helix αI in the myristoyl unbound form and
the SH2 domain. Helix αI from the structure of the isolated
kinase domain in the absence of myristoyl (PDB code 1M52) is
colored red and the new helices (αI and αI′) formed upon
binding of myristate are colored blue. Shown in shaded gray
ellipses are regions that contain isolated patches of unmodeled
electron density, potentially due to residues from the
N-terminal cap region.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2003,
112,
859-871)
copyright 2003.
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Figures were
selected
by the author.
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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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S.Ferreira-Cerca,
V.Sagar,
T.Schäfer,
M.Diop,
A.M.Wesseling,
H.Lu,
E.Chai,
E.Hurt,
and
N.Laronde-Leblanc
(2012).
ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit.
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Nat Struct Mol Biol,
19,
1316-1323.
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PDB codes:
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T.O'Hare,
M.S.Zabriskie,
A.M.Eiring,
and
M.W.Deininger
(2012).
Pushing the limits of targeted therapy in chronic myeloid leukaemia.
|
| |
Nat Rev Cancer,
12,
513-526.
|
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|
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|
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J.Yang,
N.Campobasso,
M.P.Biju,
K.Fisher,
X.Q.Pan,
J.Cottom,
S.Galbraith,
T.Ho,
H.Zhang,
X.Hong,
P.Ward,
G.Hofmann,
B.Siegfried,
F.Zappacosta,
Y.Washio,
P.Cao,
J.Qu,
S.Bertrand,
D.Y.Wang,
M.S.Head,
H.Li,
S.Moores,
Z.Lai,
K.Johanson,
G.Burton,
C.Erickson-Miller,
G.Simpson,
P.Tummino,
R.A.Copeland,
and
A.Oliff
(2011).
Discovery and characterization of a cell-permeable, small-molecule c-Abl kinase activator that binds to the myristoyl binding site.
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Chem Biol,
18,
177-186.
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PDB code:
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K.Zhang,
Y.Zhu,
X.He,
and
Y.Zhang
(2011).
Systematic screening of protein modifications in four kinases using affinity enrichment and mass spectrometry analysis with unrestrictive sequence alignment.
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Anal Chim Acta,
691,
62-67.
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M.Preyer,
P.Vigneri,
and
J.Y.Wang
(2011).
Interplay between Kinase Domain Autophosphorylation and F-Actin Binding Domain in Regulating Imatinib Sensitivity and Nuclear Import of BCR-ABL.
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PLoS One,
6,
e17020.
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|
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M.Sato,
M.Maruoka,
N.Yokota,
M.Kuwano,
A.Matsui,
M.Inada,
T.Ogawa,
N.Ishida-Kitagawa,
and
T.Takeya
(2011).
Identification and functional analysis of a new phosphorylation site (Y398) in the SH3 domain of Abi-1.
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FEBS Lett,
585,
834-840.
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M.Thai,
P.Y.Ting,
J.McLaughlin,
D.Cheng,
M.Müschen,
O.N.Witte,
and
J.Colicelli
(2011).
ABL fusion oncogene transformation and inhibitor sensitivity are mediated by the cellular regulator RIN1.
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Leukemia,
25,
290-300.
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S.Schenone,
O.Bruno,
M.Radi,
and
M.Botta
(2011).
New insights into small-molecule inhibitors of Bcr-Abl.
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Med Res Rev,
31,
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W.W.Chan,
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T.J.Rutkoski,
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R.Clark,
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K.Lazarides,
V.M.Zaleskas,
L.J.Stewart,
R.A.Van Etten,
and
D.L.Flynn
(2011).
Conformational control inhibition of the BCR-ABL1 tyrosine kinase, including the gatekeeper T315I mutant, by the switch-control inhibitor DCC-2036.
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Cancer Cell,
19,
556-568.
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PDB codes:
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A.K.Wernimont,
J.D.Artz,
P.Finerty,
Y.H.Lin,
M.Amani,
A.Allali-Hassani,
G.Senisterra,
M.Vedadi,
W.Tempel,
F.Mackenzie,
I.Chau,
S.Lourido,
L.D.Sibley,
and
R.Hui
(2010).
Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium.
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Nat Struct Mol Biol,
17,
596-601.
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PDB codes:
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A.Mehlitz,
S.Banhart,
A.P.Mäurer,
A.Kaushansky,
A.G.Gordus,
J.Zielecki,
G.Macbeath,
and
T.F.Meyer
(2010).
Tarp regulates early Chlamydia-induced host cell survival through interactions with the human adaptor protein SHC1.
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| |
J Cell Biol,
190,
143-157.
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A.Palencia,
A.Camara-Artigas,
M.T.Pisabarro,
J.C.Martinez,
and
I.Luque
(2010).
Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.
|
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J Biol Chem,
285,
2823-2833.
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PDB codes:
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C.B.McDonald,
K.L.Seldeen,
B.J.Deegan,
V.Bhat,
and
A.Farooq
(2010).
Assembly of the Sos1-Grb2-Gab1 ternary signaling complex is under allosteric control.
|
| |
Arch Biochem Biophys,
494,
216-225.
|
|
|
|
|
|
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D.W.Sherbenou,
O.Hantschel,
I.Kaupe,
S.Willis,
T.Bumm,
L.P.Turaga,
T.Lange,
K.H.Dao,
R.D.Press,
B.J.Druker,
G.Superti-Furga,
and
M.W.Deininger
(2010).
BCR-ABL SH3-SH2 domain mutations in chronic myeloid leukemia patients on imatinib.
|
| |
Blood,
116,
3278-3285.
|
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|
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|
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E.A.Placzek,
M.P.Plebanek,
A.M.Lipchik,
S.R.Kidd,
and
L.L.Parker
(2010).
A peptide biosensor for detecting intracellular Abl kinase activity using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
|
| |
Anal Biochem,
397,
73-78.
|
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|
|
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|
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F.Tsukahara,
and
Y.Maru
(2010).
Bag1 directly routes immature BCR-ABL for proteasomal degradation.
|
| |
Blood,
116,
3582-3592.
|
|
|
|
|
|
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H.Wang,
J.Blais,
D.Ron,
and
T.Cardozo
(2010).
Structural determinants of PERK inhibitor potency and selectivity.
|
| |
Chem Biol Drug Des,
76,
480-495.
|
|
|
|
|
|
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J.B.Bruning,
A.A.Parent,
G.Gil,
M.Zhao,
J.Nowak,
M.C.Pace,
C.L.Smith,
P.V.Afonine,
P.D.Adams,
J.A.Katzenellenbogen,
and
K.W.Nettles
(2010).
Coupling of receptor conformation and ligand orientation determine graded activity.
|
| |
Nat Chem Biol,
6,
837-843.
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PDB codes:
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J.Chmielecki,
M.Peifer,
P.Jia,
N.D.Socci,
K.Hutchinson,
A.Viale,
Z.Zhao,
R.K.Thomas,
and
W.Pao
(2010).
Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer.
|
| |
Nucleic Acids Res,
38,
6985-6996.
|
|
|
|
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|
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J.H.Mao,
X.Y.Sun,
J.X.Liu,
Q.Y.Zhang,
P.Liu,
Q.H.Huang,
K.K.Li,
Q.Chen,
Z.Chen,
and
S.J.Chen
(2010).
As4S4 targets RING-type E3 ligase c-CBL to induce degradation of BCR-ABL in chronic myelogenous leukemia.
|
| |
Proc Natl Acad Sci U S A,
107,
21683-21688.
|
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|
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J.S.Oakhill,
Z.P.Chen,
J.W.Scott,
R.Steel,
L.A.Castelli,
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S.L.Macaulay,
and
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(2010).
β-Subunit myristoylation is the gatekeeper for initiating metabolic stress sensing by AMP-activated protein kinase (AMPK).
|
| |
Proc Natl Acad Sci U S A,
107,
19237-19241.
|
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J.Wojcik,
O.Hantschel,
F.Grebien,
I.Kaupe,
K.L.Bennett,
J.Barkinge,
R.B.Jones,
A.Koide,
G.Superti-Furga,
and
S.Koide
(2010).
A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain.
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Nat Struct Mol Biol,
17,
519-527.
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PDB code:
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J.Zhang,
F.J.Adrián,
W.Jahnke,
S.W.Cowan-Jacob,
A.G.Li,
R.E.Iacob,
T.Sim,
J.Powers,
C.Dierks,
F.Sun,
G.R.Guo,
Q.Ding,
B.Okram,
Y.Choi,
A.Wojciechowski,
X.Deng,
G.Liu,
G.Fendrich,
A.Strauss,
N.Vajpai,
S.Grzesiek,
T.Tuntland,
Y.Liu,
B.Bursulaya,
M.Azam,
P.W.Manley,
J.R.Engen,
G.Q.Daley,
M.Warmuth,
and
N.S.Gray
(2010).
Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors.
|
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Nature,
463,
501-506.
|
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PDB code:
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K.Skobridis,
M.Kinigopoulou,
V.Theodorou,
E.Giannousi,
A.Russell,
R.Chauhan,
R.Sala,
N.Brownlow,
S.Kiriakidis,
J.Domin,
A.G.Tzakos,
and
N.J.Dibb
(2010).
Novel imatinib derivatives with altered specificity between Bcr-Abl and FMS, KIT, and PDGF receptors.
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| |
ChemMedChem,
5,
130-139.
|
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K.Zhang,
Y.Chen,
Z.Zhang,
S.Tao,
H.Zhu,
and
Y.Zhao
(2010).
Unrestrictive identification of non-phosphorylation PTMs in yeast kinases by MS and PTMap.
|
| |
Proteomics,
10,
896-903.
|
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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.
|
| |
Arch Pharm (Weinheim),
343,
193-206.
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O.Fedorov,
S.Müller,
and
S.Knapp
(2010).
The (un)targeted cancer kinome.
|
| |
Nat Chem Biol,
6,
166-169.
|
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P.Patwardhan,
and
M.D.Resh
(2010).
Myristoylation and membrane binding regulate c-Src stability and kinase activity.
|
| |
Mol Cell Biol,
30,
4094-4107.
|
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R.Krishnamurty,
and
D.J.Maly
(2010).
Biochemical mechanisms of resistance to small-molecule protein kinase inhibitors.
|
| |
ACS Chem Biol,
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|
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S.Gonfloni
(2010).
DNA damage stress response in germ cells: role of c-Abl and clinical implications.
|
| |
Oncogene,
29,
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C.Wei,
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Y.Xu,
W.Shi,
Q.Ye,
and
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(2010).
c-Abl regulates estrogen receptor alpha transcription activity through its stabilization by phosphorylation.
|
| |
Oncogene,
29,
2238-2251.
|
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|
|
|
|
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Y.Rikihisa,
M.Lin,
and
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(2010).
Type IV secretion in the obligatory intracellular bacterium Anaplasma phagocytophilum.
|
| |
Cell Microbiol,
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A.Dixit,
and
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(2009).
Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.
|
| |
PLoS Comput Biol,
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|
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|
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A.Quintás-Cardama,
and
J.Cortes
(2009).
Molecular biology of bcr-abl1-positive chronic myeloid leukemia.
|
| |
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|
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and
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(2009).
Involvement of c-Abl, p53 and the MAP kinase JNK in the cell death program initiated in A2E-laden ARPE-19 cells by exposure to blue light.
|
| |
Apoptosis,
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|
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|
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and
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Reciprocal regulation of Abl and receptor tyrosine kinases.
|
| |
Cell Signal,
21,
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|
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G.Superti-Furga,
and
J.Kuriyan
(2009).
The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2).
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| |
BMC Struct Biol,
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|
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PDB code:
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|
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J.E.Dueber,
G.C.Wu,
G.R.Malmirchegini,
T.S.Moon,
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K.L.Prather,
and
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(2009).
Synthetic protein scaffolds provide modular control over metabolic flux.
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| |
Nat Biotechnol,
27,
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J.J.Gu,
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(2009).
Abl tyrosine kinases in T-cell signaling.
|
| |
Immunol Rev,
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|
J.Zhang,
P.L.Yang,
and
N.S.Gray
(2009).
Targeting cancer with small molecule kinase inhibitors.
|
| |
Nat Rev Cancer,
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|
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K.Huang,
Y.H.Wang,
A.Brown,
and
G.Sun
(2009).
Identification of N-terminal lobe motifs that determine the kinase activity of the catalytic domains and regulatory strategies of Src and Csk protein tyrosine kinases.
|
| |
J Mol Biol,
386,
1066-1077.
|
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|
|
|
|
|
L.J.Yang,
J.Zou,
H.Z.Xie,
L.L.Li,
Y.Q.Wei,
and
S.Y.Yang
(2009).
Steered molecular dynamics simulations reveal the likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl.
|
| |
PLoS One,
4,
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|
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|
L.N.Johnson
(2009).
Protein kinase inhibitors: contributions from structure to clinical compounds.
|
| |
Q Rev Biophys,
42,
1.
|
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|
M.A.Seeliger,
P.Ranjitkar,
C.Kasap,
Y.Shan,
D.E.Shaw,
N.P.Shah,
J.Kuriyan,
and
D.J.Maly
(2009).
Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations.
|
| |
Cancer Res,
69,
2384-2392.
|
|
|
PDB codes:
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|
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|
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M.Bantscheff,
A.Scholten,
and
A.J.Heck
(2009).
Revealing promiscuous drug-target interactions by chemical proteomics.
|
| |
Drug Discov Today,
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|
P.Filippakopoulos,
S.Müller,
and
S.Knapp
(2009).
SH2 domains: modulators of nonreceptor tyrosine kinase activity.
|
| |
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PDB code:
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PDB code:
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PDB codes:
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Entropic switch regulates myristate exposure in the HIV-1 matrix protein.
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Proc Natl Acad Sci U S A,
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PDB code:
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Crystal structures of the phosphorylated and unphosphorylated kinase domains of the Cdc42-associated tyrosine kinase ACK1.
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PDB codes:
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Trafficking of Lyn through the Golgi caveolin involves the charged residues on alphaE and alphaI helices in the kinase domain.
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A novel mode of Gleevec binding is revealed by the structure of spleen tyrosine kinase.
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PDB codes:
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S.E.Hernández,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
 |
Links
