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PDBsum entry 1fpu
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Contents |
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* Residue conservation analysis
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Enzyme class:
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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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Science
289:1938-1942
(2000)
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PubMed id:
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Structural mechanism for STI-571 inhibition of abelson tyrosine kinase.
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T.Schindler,
W.Bornmann,
P.Pellicena,
W.T.Miller,
B.Clarkson,
J.Kuriyan.
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ABSTRACT
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The inadvertent activation of the Abelson tyrosine kinase (Abl) causes chronic
myelogenous leukemia (CML). A small-molecule inhibitor of Abl (STI-571) is
effective in the treatment of CML. We report the crystal structure of the
catalytic domain of Abl, complexed to a variant of STI-571. Critical to the
binding of STI-571 is the adoption by the kinase of an inactive conformation, in
which a centrally located "activation loop" is not phosphorylated. The
conformation of this loop is distinct from that in active protein kinases, as
well as in the inactive form of the closely related Src kinases. These results
suggest that compounds that exploit the distinctive inactivation mechanisms of
individual protein kinases can achieve both high affinity and high specificity.
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Selected figure(s)
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Figure 1.
Fig. 1. Crystal structure of the catalytic domain of Abelson
tyrosine kinase complexed with a variant of STI-571. (A)
Structural formula of the Abl inhibitor STI-571 (panel 1) and
the variant (panel 2) used in this crystallographic study. (B)
Ribbon representation of the three-dimensional structure of Abl
kinase domain in complex with the STI-571 variant shown in (A).
The molecular surface of the inhibitor is shown. A central
conserved region of the kinase, the catalytic segment, is shown
in green and the activation loop in magenta. (C) Ribbon
representation of the activation loop of Abl. The polypeptide
backbone of the activation loop is shown in magenta.
Hydrogen-bonding interaction are depicted by dashed lines.
Tyr393 is the site of phosphorylation within the activation
loop. (D) The polypeptide region in the vicinity of the Tyr393
is shown. Superimposed is the peptide substrate (green), as seen
in the structure of insulin receptor tyrosine kinase (IRK)
complexed with peptide substrate (14), and the activation loop
of IRK in the inactive form (light pink) (32). The figure was
generated by superimposing the catalytic segments of the two
kinases.
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Figure 3.
Fig. 3. STI-571 exploits the unique conformation of the
activation loop in the down-regulated form of Abl. Conformation
of the activation loops of Abl and the Src kinases Lck (active)
(16) and Hck (inactive) (11). Also shown is a space-filling
model of the Abl-specific inhibitor. The figure was generated by
superimposing the catalytic segments of the displayed kinases.
The structures of Lck and Hck are representative for the active
and the inactive state of Src-family tyrosine kinases,
respectively. The active form of Abl is expected to resemble
that of Lck. The activation loop is magenta, the catalytic
segment green. The conserved side chains of the Asp-Phe-Gly
motif and the tyrosine residue in the activation loop are shown
in a ball-and-stick representation.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2000,
289,
1938-1942)
copyright 2000.
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Figures were
selected
by an automated process.
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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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T.O'Hare,
M.S.Zabriskie,
A.M.Eiring,
and
M.W.Deininger
(2012).
Pushing the limits of targeted therapy in chronic myeloid leukaemia.
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Nat Rev Cancer,
12,
513-526.
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A.Tefferi
(2011).
Second-generation tyrosine kinase inhibitors in chronic myelogenous leukemia: Before or after imatinib?
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Cancer,
117,
234-237.
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D.Bixby,
and
M.Talpaz
(2011).
Seeking the causes and solutions to imatinib-resistance in chronic myeloid leukemia.
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Leukemia,
25,
7.
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E.De Braekeleer,
N.Douet-Guilbert,
D.Rowe,
N.Bown,
F.Morel,
C.Berthou,
C.Férec,
and
M.De Braekeleer
(2011).
ABL1 fusion genes in hematological malignancies: a review.
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Eur J Haematol,
86,
361-371.
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H.Liang,
T.Liu,
F.Chen,
Z.Liu,
and
S.Liu
(2011).
A full-length 3D structure for MAPK/ERK kinase 2 (MEK2).
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Sci China Life Sci,
54,
336-341.
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J.M.Diamond,
and
J.V.Melo
(2011).
Mechanisms of resistance to BCR-ABL kinase inhibitors.
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Leuk Lymphoma,
52,
12-22.
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J.Y.Blay,
and
M.von Mehren
(2011).
Nilotinib: a novel, selective tyrosine kinase inhibitor.
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Semin Oncol,
38,
S3-S9.
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M.Affer,
S.Dao,
C.Liu,
A.B.Olshen,
Q.Mo,
A.Viale,
C.L.Lambek,
T.G.Marr,
and
B.D.Clarkson
(2011).
Gene Expression Differences between Enriched Normal and Chronic Myelogenous Leukemia Quiescent Stem/Progenitor Cells and Correlations with Biological Abnormalities.
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J Oncol,
2011,
798592.
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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.
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Mol Cell,
42,
9.
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S.M.Noor,
R.Bell,
and
A.C.Ward
(2011).
Shooting the messenger: targeting signal transduction pathways in leukemia and related disorders.
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Crit Rev Oncol Hematol,
78,
33-44.
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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,
1.
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W.W.Chan,
S.C.Wise,
M.D.Kaufman,
Y.M.Ahn,
C.L.Ensinger,
T.Haack,
M.M.Hood,
J.Jones,
J.W.Lord,
W.P.Lu,
D.Miller,
W.C.Patt,
B.D.Smith,
P.A.Petillo,
T.J.Rutkoski,
H.Telikepalli,
L.Vogeti,
T.Yao,
L.Chun,
R.Clark,
P.Evangelista,
L.C.Gavrilescu,
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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Y.Y.Wang,
L.J.Zhao,
C.F.Wu,
P.Liu,
L.Shi,
Y.Liang,
S.M.Xiong,
J.Q.Mi,
Z.Chen,
R.Ren,
and
S.J.Chen
(2011).
C-KIT mutation cooperates with full-length AML1-ETO to induce acute myeloid leukemia in mice.
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Proc Natl Acad Sci U S A,
108,
2450-2455.
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A.I.Swimm,
W.Bornmann,
M.Jiang,
M.J.Imperiale,
A.E.Lukacher,
and
D.Kalman
(2010).
Abl family tyrosine kinases regulate sialylated ganglioside receptors for polyomavirus.
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J Virol,
84,
4243-4251.
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A.S.Moore,
J.Blagg,
S.Linardopoulos,
and
A.D.Pearson
(2010).
Aurora kinase inhibitors: novel small molecules with promising activity in acute myeloid and Philadelphia-positive leukemias.
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Leukemia,
24,
671-678.
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B.J.Grant,
A.A.Gorfe,
and
J.A.McCammon
(2010).
Large conformational changes in proteins: signaling and other functions.
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Curr Opin Struct Biol,
20,
142-147.
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B.Kosova,
B.Tezcanli,
H.A.Ekiz,
Z.Cakir,
N.Selvi,
A.Dalmizrak,
M.Kartal,
U.Gunduz,
and
Y.Baran
(2010).
Suppression of STAT5A increases chemotherapeutic sensitivity in imatinib-resistant and imatinib-sensitive K562 cells.
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Leuk Lymphoma,
51,
1895-1901.
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B.Oskouian,
and
J.D.Saba
(2010).
Cancer treatment strategies targeting sphingolipid metabolism.
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Adv Exp Med Biol,
688,
185-205.
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B.Yu,
I.R.Martins,
P.Li,
G.K.Amarasinghe,
J.Umetani,
M.E.Fernandez-Zapico,
D.D.Billadeau,
M.Machius,
D.R.Tomchick,
and
M.K.Rosen
(2010).
Structural and energetic mechanisms of cooperative autoinhibition and activation of Vav1.
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Cell,
140,
246-256.
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PDB code:
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C.A.Dodson,
M.Kosmopoulou,
M.W.Richards,
B.Atrash,
V.Bavetsias,
J.Blagg,
and
R.Bayliss
(2010).
Crystal structure of an Aurora-A mutant that mimics Aurora-B bound to MLN8054: insights into selectivity and drug design.
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Biochem J,
427,
19-28.
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PDB codes:
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C.J.Lord,
and
A.Ashworth
(2010).
Biology-driven cancer drug development: back to the future.
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BMC Biol,
8,
38.
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D.Arslanova,
T.Yang,
X.Xu,
S.T.Wong,
C.E.Augelli-Szafran,
and
W.Xia
(2010).
Phenotypic analysis of images of zebrafish treated with Alzheimer's gamma-secretase inhibitors.
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BMC Biotechnol,
10,
24.
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D.J.DeAngelo,
and
E.C.Attar
(2010).
Use of dasatinib and nilotinib in imatinib-resistant chronic myeloid leukemia: translating preclinical findings to clinical practice.
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Leuk Lymphoma,
51,
363-375.
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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.
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Blood,
116,
3278-3285.
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E.A.Murphy,
D.J.Shields,
K.Stoletov,
E.Dneprovskaia,
M.McElroy,
J.I.Greenberg,
J.Lindquist,
L.M.Acevedo,
S.Anand,
B.K.Majeti,
I.Tsigelny,
A.Saldanha,
B.Walsh,
R.M.Hoffman,
M.Bouvet,
R.L.Klemke,
P.K.Vogt,
L.Arnold,
W.Wrasidlo,
and
D.A.Cheresh
(2010).
Disruption of angiogenesis and tumor growth with an orally active drug that stabilizes the inactive state of PDGFRbeta/B-RAF.
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Proc Natl Acad Sci U S A,
107,
4299-4304.
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E.Weisberg,
H.G.Choi,
A.Ray,
R.Barrett,
J.Zhang,
T.Sim,
W.Zhou,
M.Seeliger,
M.Cameron,
M.Azam,
J.A.Fletcher,
M.Debiec-Rychter,
M.Mayeda,
D.Moreno,
A.L.Kung,
P.A.Janne,
R.Khosravi-Far,
J.V.Melo,
P.W.Manley,
S.Adamia,
C.Wu,
N.Gray,
and
J.D.Griffin
(2010).
Discovery of a small-molecule type II inhibitor of wild-type and gatekeeper mutants of BCR-ABL, PDGFRalpha, Kit, and Src kinases: novel type II inhibitor of gatekeeper mutants.
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Blood,
115,
4206-4216.
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PDB code:
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F.Tsukahara,
and
Y.Maru
(2010).
Bag1 directly routes immature BCR-ABL for proteasomal degradation.
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Blood,
116,
3582-3592.
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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.
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Nat Chem Biol,
6,
837-843.
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PDB codes:
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J.Colicelli
(2010).
ABL tyrosine kinases: evolution of function, regulation, and specificity.
|
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Sci Signal,
3,
re6.
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J.Eswaran,
and
S.Knapp
(2010).
Insights into protein kinase regulation and inhibition by large scale structural comparison.
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Biochim Biophys Acta,
1804,
429-432.
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K.A.Kalesh,
D.S.Sim,
J.Wang,
K.Liu,
Q.Lin,
and
S.Q.Yao
(2010).
Small molecule probes that target Abl kinase.
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Chem Commun (Camb),
46,
1118-1120.
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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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L.M.Wodicka,
P.Ciceri,
M.I.Davis,
J.P.Hunt,
M.Floyd,
S.Salerno,
X.H.Hua,
J.M.Ford,
R.C.Armstrong,
P.P.Zarrinkar,
and
D.K.Treiber
(2010).
Activation state-dependent binding of small molecule kinase inhibitors: structural insights from biochemistry.
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Chem Biol,
17,
1241-1249.
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M.L.Ballinger,
N.Osman,
K.Hashimura,
J.B.Haan,
K.Jandeleit-Dahm,
T.Allen,
L.R.Tannock,
J.C.Rutledge,
and
P.J.Little
(2010).
Imatinib inhibits vascular smooth muscle proteoglycan synthesis and reduces LDL binding in vitro and aortic lipid deposition in vivo.
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J Cell Mol Med,
14,
1408-1418.
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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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N.Zhang,
and
R.Zhong
(2010).
Structural basis for decreased affinity of Emodin binding to Val66-mutated human CK2 alpha as determined by molecular dynamics.
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J Mol Model,
16,
771-780.
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P.Filippakopoulos,
J.Qi,
S.Picaud,
Y.Shen,
W.B.Smith,
O.Fedorov,
E.M.Morse,
T.Keates,
T.T.Hickman,
I.Felletar,
M.Philpott,
S.Munro,
M.R.McKeown,
Y.Wang,
A.L.Christie,
N.West,
M.J.Cameron,
B.Schwartz,
T.D.Heightman,
N.La Thangue,
C.A.French,
O.Wiest,
A.L.Kung,
S.Knapp,
and
J.E.Bradner
(2010).
Selective inhibition of BET bromodomains.
|
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Nature,
468,
1067-1073.
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PDB codes:
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P.La Rosée,
and
A.Hochhaus
(2010).
Molecular pathogenesis of tyrosine kinase resistance in chronic myeloid leukemia.
|
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Curr Opin Hematol,
17,
91-96.
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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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P.Shi,
J.Chandra,
X.Sun,
M.Gergely,
J.E.Cortes,
G.Garcia-Manero,
R.B.Arlinghaus,
R.Lai,
and
H.M.Amin
(2010).
Inhibition of IGF-IR tyrosine kinase induces apoptosis and cell cycle arrest in imatinib-resistant chronic myeloid leukaemia cells.
|
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J Cell Mol Med,
14,
1777-1792.
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R.Krishnamurty,
and
D.J.Maly
(2010).
Biochemical mechanisms of resistance to small-molecule protein kinase inhibitors.
|
| |
ACS Chem Biol,
5,
121-138.
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R.Tanaka,
M.S.Squires,
S.Kimura,
A.Yokota,
R.Nagao,
T.Yamauchi,
M.Takeuchi,
H.Yao,
M.Reule,
T.Smyth,
J.F.Lyons,
N.T.Thompson,
E.Ashihara,
O.G.Ottmann,
and
T.Maekawa
(2010).
Activity of the multitargeted kinase inhibitor, AT9283, in imatinib-resistant BCR-ABL-positive leukemic cells.
|
| |
Blood,
116,
2089-2095.
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S.B.Gabelli,
D.Mandelker,
O.Schmidt-Kittler,
B.Vogelstein,
and
L.M.Amzel
(2010).
Somatic mutations in PI3Kalpha: structural basis for enzyme activation and drug design.
|
| |
Biochim Biophys Acta,
1804,
533-540.
|
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S.Gonfloni
(2010).
DNA damage stress response in germ cells: role of c-Abl and clinical implications.
|
| |
Oncogene,
29,
6193-6202.
|
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S.Lü,
Q.Luo,
X.Li,
J.Wu,
J.Liu,
S.Xiong,
Y.Q.Feng,
and
F.Wang
(2010).
Inhibitor screening of protein kinases using MALDI-TOF MS combined with separation and enrichment of phosphopeptides by TiO2 nanoparticle deposited capillary column.
|
| |
Analyst,
135,
2858-2863.
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S.P.Williams,
T.Karnezis,
M.G.Achen,
and
S.A.Stacker
(2010).
Targeting lymphatic vessel functions through tyrosine kinases.
|
| |
J Angiogenes Res,
2,
13.
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T.S.Girish,
and
B.Gopal
(2010).
Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states.
|
| |
J Biol Chem,
285,
29406-29415.
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PDB codes:
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T.Zhou,
L.Commodore,
W.S.Huang,
Y.Wang,
T.K.Sawyer,
W.C.Shakespeare,
T.Clackson,
X.Zhu,
and
D.C.Dalgarno
(2010).
Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl purine template.
|
| |
Chem Biol Drug Des,
75,
18-28.
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PDB codes:
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W.W.Chen,
M.Niepel,
and
P.K.Sorger
(2010).
Classic and contemporary approaches to modeling biochemical reactions.
|
| |
Genes Dev,
24,
1861-1875.
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A.Dixit,
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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.
|
|
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