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PDBsum entry 1qpd
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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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Structure
7:651-661
(1999)
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PubMed id:
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Structural analysis of the lymphocyte-specific kinase Lck in complex with non-selective and Src family selective kinase inhibitors.
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X.Zhu,
J.L.Kim,
J.R.Newcomb,
P.E.Rose,
D.R.Stover,
L.M.Toledo,
H.Zhao,
K.A.Morgenstern.
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ABSTRACT
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BACKGROUND: The lymphocyte-specific kinase Lck is a member of the Src family of
non-receptor tyrosine kinases. Lck catalyzes the initial phosphorylation of
T-cell receptor components that is necessary for signal transduction and T-cell
activation. On the basis of both biochemical and genetic studies, Lck is
considered an attractive cell-specific target for the design of novel T-cell
immunosuppressants. To date, the lack of detailed structural information on the
mode of inhibitor binding to Lck has limited the discovery of novel Lck
inhibitors. RESULTS: We report here the high-resolution crystal structures of an
activated Lck kinase domain in complex with three structurally distinct
ATP-competitive inhibitors: AMP-PNP (a non-selective, non-hydrolyzable ATP
analog); staurosporine (a potent but non-selective protein kinase inhibitor);
and PP2 (a potent Src family selective protein tyrosine kinase inhibitor).
Comparison of these structures reveals subtle but important structural changes
at the ATP-binding site. Furthermore, PP2 is found to access a deep, hydrophobic
pocket near the ATP-binding cleft of the enzyme; this binding pocket is not
occupied by either AMP-PNP or staurosporine. CONCLUSIONS: The potency of
staurosporine against Lck derives in part from an induced movement of the
glycine-rich loop of the enzyme upon binding of this ligand, which maximizes the
van der Waals interactions present in the complex. In contrast, PP2 binds
tightly and selectively to Lck and other Src family kinases by making additional
contacts in a deep, hydrophobic pocket adjacent to the ATP-binding site; the
amino acid composition of this pocket is unique to Src family kinases. The
structures of these Lck complexes offer useful structural insights as they
demonstrate that kinase selectivity can be achieved with small-molecule
inhibitors that exploit subtle topological differences among protein kinases.
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Selected figure(s)
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Figure 2.
Figure 2. Schematic representation of the hydrogen-bond
interactions and van der Waals contacts between Lck and bound
ligands: (a) AMP-PNP; (b) staurosporine; (c) PP2. Hydrogen bonds
are represented with dashed lines. The residues of Lck in
contact with the bound ligand are shown.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1999,
7,
651-661)
copyright 1999.
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Figure was
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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D.Seeliger,
and
B.L.de Groot
(2010).
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations.
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PLoS Comput Biol,
6,
e1000634.
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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.
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Chem Biol Drug Des,
75,
18-28.
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PDB codes:
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X.Zhang,
J.A.Arnott,
S.Rehman,
W.G.Delong,
A.Sanjay,
F.F.Safadi,
and
S.N.Popoff
(2010).
Src is a major signaling component for CTGF induction by TGF-beta1 in osteoblasts.
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J Cell Physiol,
224,
691-701.
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E.Oksanen,
M.P.Blakeley,
F.Bonneté,
M.T.Dauvergne,
F.Dauvergne,
and
M.Budayova-Spano
(2009).
Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase.
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J R Soc Interface,
6,
S599-S610.
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K.E.Muratore,
M.A.Seeliger,
Z.Wang,
D.Fomina,
J.Neiswinger,
J.J.Havranek,
D.Baker,
J.Kuriyan,
and
P.A.Cole
(2009).
Comparative analysis of mutant tyrosine kinase chemical rescue.
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Biochemistry,
48,
3378-3386.
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PDB code:
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M.A.Meyn,
and
T.E.Smithgall
(2009).
Chemical genetics identifies c-Src as an activator of primitive ectoderm formation in murine embryonic stem cells.
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Sci Signal,
2,
ra64.
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N.K.Williams,
I.S.Lucet,
S.P.Klinken,
E.Ingley,
and
J.Rossjohn
(2009).
Crystal Structures of the Lyn Protein Tyrosine Kinase Domain in Its Apo- and Inhibitor-bound State.
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J Biol Chem,
284,
284-291.
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PDB codes:
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R.Barouch-Bentov,
J.Che,
C.C.Lee,
Y.Yang,
A.Herman,
Y.Jia,
A.Velentza,
J.Watson,
L.Sternberg,
S.Kim,
N.Ziaee,
A.Miller,
C.Jackson,
M.Fujimoto,
M.Young,
S.Batalov,
Y.Liu,
M.Warmuth,
T.Wiltshire,
M.P.Cooke,
and
K.Sauer
(2009).
A conserved salt bridge in the G loop of multiple protein kinases is important for catalysis and for in vivo Lyn function.
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Mol Cell,
33,
43-52.
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R.M.Eglen,
and
T.Reisine
(2009).
The current status of drug discovery against the human kinome.
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Assay Drug Dev Technol,
7,
22-43.
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S.A.Austin,
M.A.Sens,
and
C.K.Combs
(2009).
Amyloid precursor protein mediates a tyrosine kinase-dependent activation response in endothelial cells.
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J Neurosci,
29,
14451-14462.
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Z.Kiliç,
Y.G.Isgör,
and
S.Olgen
(2009).
Synthesis and pp60c-Src tyrosine kinase inhibitory activities of novel indole-3-imine and amine derivatives substituted at N1 and C5.
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Arch Pharm (Weinheim),
342,
333-343.
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Z.Kiliç,
Y.G.Işgör,
and
S.Olgen
(2009).
Evaluation of new indole and bromoindole derivatives as pp60(c-Src) tyrosine kinase inhibitors.
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Chem Biol Drug Des,
74,
397-404.
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Z.Tang,
S.Jiang,
R.Du,
E.T.Petri,
A.El-Telbany,
P.S.Chan,
T.Kijima,
S.Dietrich,
K.Matsui,
M.Kobayashi,
S.Sasada,
N.Okamoto,
H.Suzuki,
K.Kawahara,
T.Iwasaki,
K.Nakagawa,
I.Kawase,
J.G.Christensen,
T.Hirashima,
B.Halmos,
R.Salgia,
T.J.Boggon,
J.A.Kern,
and
P.C.Ma
(2009).
Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.
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Oncogene,
28,
518-533.
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C.Harbert,
J.Marshall,
S.Soh,
and
K.Steger
(2008).
Development of a HTRF kinase assay for determination of Syk activity.
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Curr Chem Genomics,
1,
20-26.
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M.C.Jecklin,
D.Touboul,
C.Bovet,
A.Wortmann,
and
R.Zenobi
(2008).
Which electrospray-based ionization method best reflects protein-ligand interactions found in solution? a comparison of ESI, nanoESI, and ESSI for the determination of dissociation constants with mass spectrometry.
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J Am Soc Mass Spectrom,
19,
332-343.
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M.D.Jacobs,
P.R.Caron,
and
B.J.Hare
(2008).
Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: structure of lck/imatinib complex.
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Proteins,
70,
1451-1460.
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PDB code:
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S.H.Jia,
J.Parodo,
A.Kapus,
O.D.Rotstein,
and
J.C.Marshall
(2008).
Dynamic regulation of neutrophil survival through tyrosine phosphorylation or dephosphorylation of caspase-8.
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J Biol Chem,
283,
5402-5413.
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S.Olgen,
Y.G.Isgör,
and
T.Coban
(2008).
Synthesis and Activity of Novel 5-Substituted Pyrrolo[2,3-d]pyrimidine Analogues as pp60(c-Src) Tyrosine Kinase Inhibitors.
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Arch Pharm (Weinheim),
341,
113-120.
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Y.Mori,
T.Hirokawa,
K.Aoki,
H.Satomi,
S.Takeda,
M.Aburada,
and
K.Miyamoto
(2008).
Structure activity relationships of quinoxalin-2-one derivatives as platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors, derived from molecular modeling.
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Chem Pharm Bull (Tokyo),
56,
682-687.
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C.H.Yun,
T.J.Boggon,
Y.Li,
M.S.Woo,
H.Greulich,
M.Meyerson,
and
M.J.Eck
(2007).
Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity.
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Cancer Cell,
11,
217-227.
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PDB codes:
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D.Lietha,
X.Cai,
D.F.Ceccarelli,
Y.Li,
M.D.Schaller,
and
M.J.Eck
(2007).
Structural basis for the autoinhibition of focal adhesion kinase.
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Cell,
129,
1177-1187.
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PDB codes:
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G.Bunkoczi,
E.Salah,
P.Filippakopoulos,
O.Fedorov,
S.Müller,
F.Sobott,
S.A.Parker,
H.Zhang,
W.Min,
B.E.Turk,
and
S.Knapp
(2007).
Structural and functional characterization of the human protein kinase ASK1.
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Structure,
15,
1215-1226.
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PDB code:
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S.W.Cowan-Jacob,
G.Fendrich,
A.Floersheimer,
P.Furet,
J.Liebetanz,
G.Rummel,
P.Rheinberger,
M.Centeleghe,
D.Fabbro,
and
P.W.Manley
(2007).
Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia.
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Acta Crystallogr D Biol Crystallogr,
63,
80-93.
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PDB codes:
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Z.Pan,
H.Scheerens,
S.J.Li,
B.E.Schultz,
P.A.Sprengeler,
L.C.Burrill,
R.V.Mendonca,
M.D.Sweeney,
K.C.Scott,
P.G.Grothaus,
D.A.Jeffery,
J.M.Spoerke,
L.A.Honigberg,
P.R.Young,
S.A.Dalrymple,
and
J.T.Palmer
(2007).
Discovery of Selective Irreversible Inhibitors for Bruton's Tyrosine Kinase.
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ChemMedChem,
2,
58-61.
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A.Levitzki,
and
E.Mishani
(2006).
Tyrphostins and other tyrosine kinase inhibitors.
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Annu Rev Biochem,
75,
93.
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C.Sánchez,
C.Méndez,
and
J.A.Salas
(2006).
Indolocarbazole natural products: occurrence, biosynthesis, and biological activity.
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Nat Prod Rep,
23,
1007-1045.
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C.S.Page,
and
P.A.Bates
(2006).
Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?
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J Comput Chem,
27,
1990-2007.
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D.Dalgarno,
T.Stehle,
S.Narula,
P.Schelling,
M.R.van Schravendijk,
S.Adams,
L.Andrade,
J.Keats,
M.Ram,
L.Jin,
T.Grossman,
I.MacNeil,
C.Metcalf,
W.Shakespeare,
Y.Wang,
T.Keenan,
R.Sundaramoorthi,
R.Bohacek,
M.Weigele,
and
T.Sawyer
(2006).
Structural basis of Src tyrosine kinase inhibition with a new class of potent and selective trisubstituted purine-based compounds.
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Chem Biol Drug Des,
67,
46-57.
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PDB codes:
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D.E.Danley
(2006).
Crystallization to obtain protein-ligand complexes for structure-aided drug design.
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Acta Crystallogr D Biol Crystallogr,
62,
569-575.
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E.Ozkirimli,
and
C.B.Post
(2006).
Src kinase activation: A switched electrostatic network.
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Protein Sci,
15,
1051-1062.
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S.Olgen
(2006).
Comparison of some 3-(substituted-benzylidene)-1,3-dihydroindolin derivatives as ligands of tyrosine kinase based on binding mode studies and biological assay.
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Arch Pharm Res,
29,
1006-1017.
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T.J.Zhou,
L.G.Sun,
Y.Gao,
and
E.J.Goldsmith
(2006).
Crystal structure of the MAP3K TAO2 kinase domain bound by an inhibitor staurosporine.
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Acta Biochim Biophys Sin (Shanghai),
38,
385-392.
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PDB code:
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A.Gill,
A.Cleasby,
and
H.Jhoti
(2005).
The discovery of novel protein kinase inhibitors by using fragment-based high-throughput x-ray crystallography.
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Chembiochem,
6,
506-512.
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M.S.Cohen,
C.Zhang,
K.M.Shokat,
and
J.Taunton
(2005).
Structural bioinformatics-based design of selective, irreversible kinase inhibitors.
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Science,
308,
1318-1321.
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N.Tapinos,
and
A.Rambukkana
(2005).
Insights into regulation of human Schwann cell proliferation by Erk1/2 via a MEK-independent and p56Lck-dependent pathway from leprosy bacilli.
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Proc Natl Acad Sci U S A,
102,
9188-9193.
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O.Prien
(2005).
Target-family-oriented focused libraries for kinases--conceptual design aspects and commercial availability.
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Chembiochem,
6,
500-505.
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P.A.Sims,
C.F.Wong,
D.Vuga,
J.A.McCammon,
and
B.M.Sefton
(2005).
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems.
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J Comput Chem,
26,
668-681.
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S.Barrett,
S.Bartlett,
A.Bolt,
A.Ironmonger,
C.Joce,
A.Nelson,
and
T.Woodhall
(2005).
Configurational stability of bisindolylmaleimide cyclophanes: from conformers to the first configurationally stable, atropisomeric bisindolylmaleimides.
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Chemistry,
11,
6277-6285.
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T.J.Boggon,
Y.Li,
P.W.Manley,
and
M.J.Eck
(2005).
Crystal structure of the Jak3 kinase domain in complex with a staurosporine analog.
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Blood,
106,
996.
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PDB code:
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U.Egner,
J.Krätzschmar,
B.Kreft,
H.D.Pohlenz,
and
M.Schneider
(2005).
The target discovery process.
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Chembiochem,
6,
468-479.
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A.Giannini,
and
M.J.Bijlmakers
(2004).
Regulation of the Src family kinase Lck by Hsp90 and ubiquitination.
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Mol Cell Biol,
24,
5667-5676.
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K.Kasahara,
Y.Nakayama,
K.Ikeda,
Y.Fukushima,
D.Matsuda,
S.Horimoto,
and
N.Yamaguchi
(2004).
Trafficking of Lyn through the Golgi caveolin involves the charged residues on alphaE and alphaI helices in the kinase domain.
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J Cell Biol,
165,
641-652.
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L.Jin,
S.Pluskey,
E.C.Petrella,
S.M.Cantin,
J.C.Gorga,
M.J.Rynkiewicz,
P.Pandey,
J.E.Strickler,
R.E.Babine,
D.T.Weaver,
and
K.J.Seidl
(2004).
The three-dimensional structure of the ZAP-70 kinase domain in complex with staurosporine: implications for the design of selective inhibitors.
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J Biol Chem,
279,
42818-42825.
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PDB code:
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M.Gassel,
C.B.Breitenlechner,
N.König,
R.Huber,
R.A.Engh,
and
D.Bossemeyer
(2004).
The protein kinase C inhibitor bisindolyl maleimide 2 binds with reversed orientations to different conformations of protein kinase A.
|
| |
J Biol Chem,
279,
23679-23690.
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PDB code:
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S.Atwell,
J.M.Adams,
J.Badger,
M.D.Buchanan,
I.K.Feil,
K.J.Froning,
X.Gao,
J.Hendle,
K.Keegan,
B.C.Leon,
H.J.Müller-Dieckmann,
V.L.Nienaber,
B.W.Noland,
K.Post,
K.R.Rajashankar,
A.Ramos,
M.Russell,
S.K.Burley,
and
S.G.Buchanan
(2004).
A novel mode of Gleevec binding is revealed by the structure of spleen tyrosine kinase.
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J Biol Chem,
279,
55827-55832.
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PDB codes:
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D.M.Browe,
and
C.M.Baumgarten
(2003).
Stretch of beta 1 integrin activates an outwardly rectifying chloride current via FAK and Src in rabbit ventricular myocytes.
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J Gen Physiol,
122,
689-702.
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E.De Moliner,
N.R.Brown,
and
L.N.Johnson
(2003).
Alternative binding modes of an inhibitor to two different kinases.
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| |
Eur J Biochem,
270,
3174-3181.
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PDB code:
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G.Scapin,
S.B.Patel,
J.Lisnock,
J.W.Becker,
and
P.V.LoGrasso
(2003).
The structure of JNK3 in complex with small molecule inhibitors: structural basis for potency and selectivity.
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| |
Chem Biol,
10,
705-712.
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PDB codes:
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J.L.Hays,
and
S.J.Watowich
(2003).
Oligomerization-induced modulation of TPR-MET tyrosine kinase activity.
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| |
J Biol Chem,
278,
27456-27463.
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L.Briese,
and
D.Willbold
(2003).
Structure determination of human Lck unique and SH3 domains by nuclear magnetic resonance spectroscopy.
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BMC Struct Biol,
3,
3.
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PDB code:
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T.Pedron,
R.Girard,
and
R.Chaby
(2003).
TLR4-dependent lipopolysaccharide-induced shedding of tumor necrosis factor receptors in mouse bone marrow granulocytes.
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| |
J Biol Chem,
278,
20555-20564.
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A.Ogawa,
Y.Takayama,
H.Sakai,
K.T.Chong,
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Where a reference describes a PDB structure, the PDB
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